git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9823 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/if.html

@@ -38,7 +38,7 @@ if "${eng} > ${eng_previous}" then "jump file1" else "jump file2"
 </PRE>
 <P><B>Description:</B>
 </P>
-<P>This command provides an in-then-else capability within an input
+<P>This command provides an if-then-else capability within an input
 script.  A Boolean expression is evaluted and the result is TRUE or
 FALSE.  Note that as in the examples above, the expression can contain
 variables, as defined by the <A HREF = "variable.html">variable</A> command, which
@@ -51,7 +51,7 @@ commands (t1, t2, ..., tN) are executed.  If it is FALSE, then Boolean
 expressions associated with successive elif keywords are evaluated
 until one is found to be true, in which case its commands (f1, f2,
 ..., fN) are executed.  If no Boolean expression is TRUE, then the
-commands associated witht the else keyword, namely (e1, e2, ..., eN),
+commands associated with the else keyword, namely (e1, e2, ..., eN),
 are executed.  The elif and else keywords and their associated
 commands are optional.  If they aren't specified and the initial
 Boolean expression is FALSE, then no commands are executed.

doc/if.txt

@@ -35,7 +35,7 @@ if "$\{eng\} > $\{eng_previous\}" then "jump file1" else "jump file2" :pre
 
 [Description:]
 
-This command provides an in-then-else capability within an input
+This command provides an if-then-else capability within an input
 script.  A Boolean expression is evaluted and the result is TRUE or
 FALSE.  Note that as in the examples above, the expression can contain
 variables, as defined by the "variable"_variable.html command, which
@@ -48,7 +48,7 @@ commands (t1, t2, ..., tN) are executed.  If it is FALSE, then Boolean
 expressions associated with successive elif keywords are evaluated
 until one is found to be true, in which case its commands (f1, f2,
 ..., fN) are executed.  If no Boolean expression is TRUE, then the
-commands associated witht the else keyword, namely (e1, e2, ..., eN),
+commands associated with the else keyword, namely (e1, e2, ..., eN),
 are executed.  The elif and else keywords and their associated
 commands are optional.  If they aren't specified and the initial
 Boolean expression is FALSE, then no commands are executed.

tools/moltemplate/LICENSE.TXT

@@ -0,0 +1,28 @@
+
+Author: Andrew Jewett, Shea Group, http://www.chem.ucsb.edu/~sheagroup/
+Copyright (c) 2013, Regents of the University of California
+All rights reserved.
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+  * Redistributions of source code must retain the above copyright notice, 
+    this list of conditions and the following disclaimer.
+  * Redistributions in binary form must reproduce the above copyright notice, 
+    this list of conditions and the following disclaimer in the documentation 
+    and/or other materials provided with the distribution.
+  * Neither the name of the University of California, Santa Barbara nor the 
+    names of its contributors may be used to endorse or promote products 
+    derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF 
+THE POSSIBILITY OF SUCH DAMAGE.
+

tools/moltemplate/README.TXT

@@ -0,0 +1,61 @@
+   --  Description:  --
+
+Moltemplate is a cross-platform text-based molecule builder for LAMMPS. 
+
+   --  Typical usage:  --
+
+moltemplate.sh [-atomstyle style] [-pdb/-xyz coord_file]  file.lt
+
+   --  Web page:  --
+
+Documentation, examples, and supporting code can be downloaded at:
+
+    http://www.moltemplate.org
+The most up-to-date version of moltemplate can be downloaded here.
+(After download, you can unpack the archive using:
+    tar xzf moltemplate_2012-3-31.tar.gz
+The date will vary from version to version.)
+
+----------------------------------------------------
+----------  INSTALLATION INSTRUCTIONS:  ------------
+----------------------------------------------------
+
+This directory should contain two folders:
+    src/       <-- location of all python and bash scripts
+    common/    <-- location of shared force fields and molecules 
+
+The ``moltemplate.sh'' script and the python scripts that it invokes are 
+located in the ``src/'' subdirectory.  You should update your PATH environment 
+variable to include this directory.  
+
+If you do not know what a PATH environment variable is, read:
+    http://www.linfo.org/path_env_var.html
+(I receive this question often.)
+
+It is also a good idea to set your MOLTEMPLATE_PATH environment variable to 
+point to the ``common/'' subdirectory.
+(Force fields and commonly used molecules will eventually be located here.)
+
+   --  Installation example ---
+
+Suppose the directory with this README.TXT file is located at ~/moltemplate.
+
+If you use the bash shell, typically you would edit your 
+~/.profile, ~/.bash_profile or ~/.bashrc files to contain the following lines:
+    export PATH="$PATH:$HOME/moltemplate/src"
+    export MOLTEMPLATE_PATH="$HOME/moltemplate/common"
+If you use the tcsh shell, typically you would edit your 
+~/.login, ~/.cshrc, or ~/.tcshrc files to contain the following lines:
+    setenv PATH "$PATH:$HOME/moltemplate/src"
+    setenv MOLTEMPLATE_PATH "$HOME/moltemplate/common"
+
+   --  Requirements:  --
+
+Moltemplate requires the Bourne-shell, and a recent version of python 
+(2.7, 3.0 or higher), and can run on OS X, linux, or windows (if a 
+suitable shell environment has been installed).
+
+   --  License:  --
+
+Moltemplate is available under the terms of the open-source 3-clause BSD 
+license.  (See LICENSE.TXT.)

tools/moltemplate/common/graphene.lt

@@ -0,0 +1,106 @@
+# This file contains a unit cell for building graphene and nanotubes
+#
+#
+#  The 2AtomCellAlignX "molecule" defined below is a minimal unit cell for any
+# hexagonal tesselation in 2-dimensions.  (See "graphene_unit_cell.jpg")
+# Surfaces constructed with this unit cell can be flat or curved into tubes.
+# The distance between nearest-neighbor carbon atoms (ie the length of a 
+# carbon-carbon bond) is equal to "d" which I set to 1.420 Angstroms.
+#
+#    d = length of each hexagon's side = 1.42 Angstroms
+#    L = length of each hexagon = 2*d  = 2.84 Angstroms
+#    W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms
+#
+# Consequently, the Lattice-cell vectors for singe-layer graphene are:
+#   (2.4595121467478,    0,     0)      (aligned with X axis)
+#   (1.2297560733739,  2.13,    0)      (2.13 = 1.5*d)
+# So, to build a sheet of graphite, you could use:
+#   sheet = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0)
+#                                        [10].move(1.2297560733739,2.13,0)
+
+
+
+
+Graphene {
+
+  2AtomCellAlignX
+  {
+    # atomID   molID     atomType charge       x               y       z
+    write("Data Atoms") {
+      $atom:C1  $mol:...  @atom:../C   0.0  -0.61487803668695 -0.355  0.0
+      $atom:C2  $mol:...  @atom:../C   0.0   0.61487803668695  0.355  0.0
+    }
+  }
+
+  # Now define properties of the Carbon graphene atom
+
+  write_once("In Init") {
+    pair_style hybrid  lj/charmm/coul/charmm  9.0 10.0
+  }
+
+  write_once("Data Masses") {
+    @atom:C  12.0
+  }
+
+  write_once("In Settings") {
+    #              i       j                              epsilon     sigma 
+    pair_coeff  @atom:C @atom:C  lj/charmm/coul/charmm   0.068443     3.407
+
+    # These Lennard-Jones parameters come from
+    #  R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus,
+    #  Chem Phys Lett, 348:187 (2001)
+
+    # Define a group consisting of only carbon atoms in graphene molecules
+    group Cgraphene type @atom:C
+  }
+
+  # Notice that the two atoms in the unit-cell above lie in the XY plane.
+  # (Their z-coordinate is zero).  It's also useful to have a version of 
+  # this object which lies in the XZ plan.  So we define this below:
+
+  2AtomCellAlignXZ = 2AtomCellAlignX.rot(90,1,0,0)
+
+} # Graphene
+
+
+
+
+
+
+
+
+
+
+# ------------   Graphite  -----------
+#
+# Note: For graphite: sheets stacked in the Z direction are separated by a
+#       distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction
+#       by a distance of d (1.42 Angstroms).  To add additional graphene layers
+#       you could use:
+#   sheet2 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0)
+#                                         [10].move(1.2297560733739,2.13,0)
+#   sheet2[*][*].move(0,  1.42, 3.35)
+#   sheet3 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0)
+#                                         [10].move(1.2297560733739,2.13,0)
+#   sheet3[*][*].move(0, -1.42, 6.70)
+#   etc...
+#       However, to build a thick sheet of graphite, it would 
+#       be more efficient to use a 4-atom unit cell:
+#
+#Graphene {
+#  GraphiteCell {
+#    # atomID   molID     atomType charge       x               y       z
+#    write("Data Atoms") {
+#      $atom:C1  $mol:...  @atom:../C   0.0  -0.61487803668695 -0.355  0.0
+#      $atom:C2  $mol:...  @atom:../C   0.0   0.61487803668695  0.355  0.0
+#      $atom:C3  $mol:...  @atom:../C   0.0  -0.61487803668695  1.065  3.35
+#      $atom:C4  $mol:...  @atom:../C   0.0   0.61487803668695  1.775  3.35
+#    }
+#  } # GraphiteCell
+#}
+#
+# Then you could create a thick sheet of graphite this way:
+#
+#   graphite = new Graphene/GraphiteCell [10].move(2.4595121467478,0,0)
+#                                        [10].move(1.2297560733739,2.13,0)
+#                                        [5].move(0,0,6.70)

tools/moltemplate/common/spce.lt

@@ -0,0 +1,52 @@
+# file "spce.lt" 
+#
+#    H1     H2
+#      \   /
+#        O
+
+SPCE {
+
+  write_once("In Init") {
+    # -- Default styles (for solo "SPCE" water) --
+    units        real
+    atom_style   full
+    # (Hybrid force fields were not necessary but are used for portability.)
+    pair_style   hybrid lj/charmm/coul/long 9.0 10.0 10.0
+    bond_style   hybrid harmonic
+    angle_style  hybrid harmonic
+    kspace_style pppm 0.0001
+    pair_modify  mix arithmetic
+  }
+
+  write("Data Atoms") {
+    $atom:O  $mol:. @atom:O -0.8476  0.0000000 0.00000 0.000000
+    $atom:H1 $mol:. @atom:H  0.4238  0.8164904 0.00000  0.5773590
+    $atom:H2 $mol:. @atom:H  0.4238  -0.8164904 0.00000 0.5773590
+  }
+
+  write_once("Data Masses") {
+    @atom:O 15.9994
+    @atom:H 1.008
+  }
+
+  write("Data Bonds") {
+    $bond:OH1 @bond:OH $atom:O $atom:H1
+    $bond:OH2 @bond:OH $atom:O $atom:H2
+  }
+
+  write("Data Angles") {
+    $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
+  }
+
+  write_once("In Settings") {
+    bond_coeff   @bond:OH     harmonic                 1000.0  1.0 
+    angle_coeff  @angle:HOH   harmonic                 1000.0  109.47
+    pair_coeff   @atom:O @atom:O  lj/charmm/coul/long  0.1553  3.166 
+    pair_coeff   @atom:H @atom:H  lj/charmm/coul/long  0.0     2.058
+    group spce type  @atom:O  @atom:H
+    fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH
+    # (Remember to "unfix" fSHAKE during minimization.)
+  }
+
+} # end of definition of "SPCE" water molecule type
+

tools/moltemplate/common/spce_ice_rect8.lt

@@ -0,0 +1,57 @@
+# This ice (1h) unit cell is rectangular and contains 8 water molecules.
+# (Coordinates and cell dimensions converted were from a PDB file.)
+# The dimensions of the unit cell (in Angstroms) are:  4.521  7.832  7.362
+
+
+import "spce.lt"    # <-- define the "SPCE" molecule
+
+SpceIceRect8 {
+
+  # Create a 3-dimensional array of 8 water molecules
+
+  wat = new SPCE[2][2][2]
+
+  # Array indices will be correlated with position [xindex][yindex][zindex]
+
+  # You can overwrite coordinates of atoms after they were created this way:
+  # (Order is not important)
+  #          atom-ID         molecule-ID      atomType    charge  newX   newY   newZ
+
+  write("Data Atoms") {
+    $atom:wat[1][0][0]/O  $mol:wat[1][0][0] @atom:SPCE/O -0.8476  3.391  1.305  1.381
+    $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H  0.4238  3.391  0.370  1.710
+    $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H  0.4238  2.582  1.772  1.710
+    $atom:wat[1][0][1]/O  $mol:wat[1][0][1] @atom:SPCE/O -0.8476  3.391  1.305  5.981
+    $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H  0.4238  3.391  1.305  6.970
+    $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H  0.4238  4.200  1.772  5.652
+    $atom:wat[0][0][0]/O  $mol:wat[0][0][0] @atom:SPCE/O -0.8476  1.131  2.611  2.300
+    $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H  0.4238  1.131  2.611  3.289
+    $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H  0.4238  0.320  2.143  1.971
+    $atom:wat[0][0][1]/O  $mol:wat[0][0][1] @atom:SPCE/O -0.8476  1.131  2.611  5.061
+    $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H  0.4238  1.940  2.143  5.391
+    $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H  0.4238  1.131  3.546  5.391
+    $atom:wat[0][1][0]/O  $mol:wat[0][1][0] @atom:SPCE/O -0.8476  1.131  5.221  1.381
+    $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H  0.4238  1.131  4.286  1.710
+    $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H  0.4238  0.320  5.688  1.710
+    $atom:wat[0][1][1]/O  $mol:wat[0][1][1] @atom:SPCE/O -0.8476  1.131  5.221  5.981
+    $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H  0.4238  1.131  5.221  6.970
+    $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H  0.4238  1.940  5.688  5.652
+    $atom:wat[1][1][0]/O  $mol:wat[1][1][0] @atom:SPCE/O -0.8476  3.391  6.526  2.300
+    $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H  0.4238  3.391  6.526  3.289
+    $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H  0.4238  2.582  6.058  1.971
+    $atom:wat[1][1][1]/O  $mol:wat[1][1][1] @atom:SPCE/O -0.8476  3.391  6.526  5.061
+    $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H  0.4238  4.200  6.058  5.391
+    $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H  0.4238  3.391  7.462  5.391
+  }
+} # IceRect8
+
+#    Credit goes to Martin Chaplin.
+#    These coordinates were orignally downloaded from Martin Chaplin's      
+#    website: http://www.btinternet.com/~martin.chaplin/ice1h.html        
+#    ... and then they were stretched independently in the xy and z       
+#    directions in order to match the lattice parameters measured by      
+#    Rottger et al.,                                                      
+#   "Lattice constants and thermal expansion of H2O and D2O ice Ih"      
+#    between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648         
+#    I am using the lattice constants measured at temperature 265K        
+#    (and pressure=100Torr).                                              

tools/moltemplate/common/tip3p_attempts/README.TXT

@@ -0,0 +1,13 @@
+This directory contains two LT files corresponding to 
+different versions of TIP3P:
+
+tip3pcharmm.lt # The implementation of TIP3P used by CHARMM (I think).
+tip3p2004.lt   # The newer Price & Brooks, J. Chem Phys 2004 model 
+               # which uses long-range coulombics
+
+I have not tested these files so I moved them here.
+(If you have tested these files, and they work, or if you have other comments 
+or suggestions, feel free to email me at jewett.aij at gmail dot com.)
+
+Andrew
+2012-10-20

tools/moltemplate/common/tip3p_attempts/tip3p2004.lt

@@ -0,0 +1,88 @@
+# file "tip3p2004.lt" 
+#
+#    H1     H2
+#      \   /
+#        O
+#
+# I think this is the TIP3P water described in the paper by
+# Daniel J. Price and Charles L. Brooks III
+# J. Chem. Phys., 121(20): 10096 (2004)
+# Specifically I think it refers to the "Model B" version of long-range TIP3P
+# described in the 3rd-to-last column of "Table I", on p.10099.
+
+TIP3P2004 {
+
+  write_once("In Init") {
+    # -- Default styles (for solo "TIP3P2004" water) --
+    units        real
+    atom_style   full
+
+    pair_style   hybrid lj/charmm/coul/long 10.0 10.5 10.5
+    bond_style   hybrid harmonic
+    angle_style  hybrid harmonic
+    kspace_style pppm 0.0001
+    pair_modify  mix arithmetic
+  }
+
+  write("Data Atoms") {
+    $atom:O  $mol:. @atom:O -0.830   0.0000000   0.00000 0.000000
+    $atom:H1 $mol:. @atom:H  0.415   0.756950327 0.00000 0.5858822766
+    $atom:H2 $mol:. @atom:H  0.415  -0.756950327 0.00000 0.5858822766
+  }
+
+  write_once("Data Masses") {
+    @atom:O 15.9994
+    @atom:H 1.008
+  }
+
+  write("Data Bonds") {
+    $bond:OH1 @bond:OH $atom:O $atom:H1
+    $bond:OH2 @bond:OH $atom:O $atom:H2
+  }
+
+  write("Data Angles") {
+    $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
+  }
+
+  write_once("In Settings") {
+    bond_coeff  @bond:OH         harmonic            450.0  0.9572
+    angle_coeff @angle:HOH       harmonic             55.0  104.52
+
+    #########################################################################
+    ####  There are two choices for for the O-O interactions
+    #########################################################################
+    ####  O-O nonbonded interactions
+    #   For the 1983 Jorgensen version of TIP3P use:
+    # pair_coeff  @atom:O @atom:O  lj/charmm/coul/charmm 0.1521 3.1507
+    #   For the 2004 Price & Brooks version of TIP3P use:
+    pair_coeff  @atom:O @atom:O  lj/charmm/coul/charmm 0.102 3.188
+    #########################################################################
+    ####  There are three choices for for the O-H and H-H interactions
+    #########################################################################
+    #### 1) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter
+    pair_coeff  @atom:H @atom:H  lj/charmm/coul/charmm 0.0460 0.4000
+    pair_coeff  @atom:O @atom:H  lj/charmm/coul/charmm 0.0836 1.7753 #arithmetic
+    #########################################################################
+    #### 2) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter,
+    ####    If you want to use this, uncomment the following two lines:
+    # pair_coeff  @atom:H @atom:H  lj/charmm/coul/charmm 0.0460 0.4000
+    # pair_coeff  @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric
+    #########################################################################
+    #### 3) The original Jorgensen 1983 parameterization has no OH or HH 
+    #      lennard-jones interactions. For this behavior, uncomment these lines:
+    # pair_coeff  @atom:H @atom:H  lj/charmm/coul/charmm 0.00 0.4000
+    # pair_coeff  @atom:O @atom:H lj/charmm/coul/charmm  0.00 1.7753
+    #########################################################################
+
+    # Define a group for the tip3p water molecules:
+    group tip3p type  @atom:O  @atom:H
+
+    # Optional: Constrain the angles and distances.
+    #           (Most implementations use this, but it is optional.)
+    fix fSHAKE tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH
+    # (Remember to "unfix" fSHAKE during minimization.)
+
+  }
+
+} # "TIP3P2004" water molecule type
+

tools/moltemplate/common/tip3p_attempts/tip3pcharmm.lt

@@ -0,0 +1,91 @@
+# file "tip3p_charmm.lt" 
+#
+#    H1     H2
+#      \   /
+#        O
+#
+# I think this is the TIP3P water model used by CHARMM (and probably AMBER)
+# It is (mostly) based on this paper:
+# Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983)
+
+TIP3Pcharmm {
+
+  write_once("In Init") {
+    # -- Default styles (for solo "TIP3Pcharmm" water) --
+    units        real
+    atom_style   full
+
+    # I'm not sure exactly which cutoffs distances are traditionally used in
+    # the TIP3P water model used by CHARMM.  
+    # (See the Price JCP 2004 paper for a review.)
+    # pair_style   hybrid lj/charmm/coul/charmm 7.5 8.0 10.0 10.5
+    # Try this instead:
+    pair_style   hybrid lj/charmm/coul/charmm 10.0 10.5 10.0 10.5
+
+    bond_style   hybrid harmonic
+    angle_style  hybrid harmonic
+    pair_modify  mix arithmetic
+  }
+
+  write("Data Atoms") {
+    $atom:O  $mol:. @atom:O -0.834   0.0000000   0.00000 0.000000
+    $atom:H1 $mol:. @atom:H  0.417   0.756950327 0.00000 0.5858822766
+    $atom:H2 $mol:. @atom:H  0.417  -0.756950327 0.00000 0.5858822766
+  }
+
+  write_once("Data Masses") {
+    @atom:O 15.9994
+    @atom:H 1.008
+  }
+
+  write("Data Bonds") {
+    $bond:OH1 @bond:OH $atom:O $atom:H1
+    $bond:OH2 @bond:OH $atom:O $atom:H2
+  }
+
+  write("Data Angles") {
+    $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
+  }
+
+  write_once("In Settings") {
+    bond_coeff  @bond:OH         harmonic            450.0  0.9572
+    angle_coeff @angle:HOH       harmonic             55.0  104.52
+
+    #########################################################################
+    ####  There are two choices for for the O-O interactions
+    #########################################################################
+    ####  O-O nonbonded interactions
+    #   For the 1983 Jorgensen version of TIP3P use:
+    pair_coeff  @atom:O @atom:O  lj/charmm/coul/charmm 0.1521 3.1507
+    #   For the 2004 Price & Brooks version of TIP3P use:
+    # pair_coeff  @atom:O @atom:O  lj/charmm/coul/charmm 0.102 3.188
+    #########################################################################
+    ####  There are three choices for for the O-H and H-H interactions
+    #########################################################################
+    #### 1) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter
+    pair_coeff  @atom:H @atom:H  lj/charmm/coul/charmm 0.0460 0.4000
+    pair_coeff  @atom:O @atom:H  lj/charmm/coul/charmm 0.0836 1.7753 #arithmetic
+    #########################################################################
+    #### 2) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter,
+    ####    If you want to use this, uncomment the following two lines:
+    # pair_coeff  @atom:H @atom:H  lj/charmm/coul/charmm 0.0460 0.4000
+    # pair_coeff  @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric
+    #########################################################################
+    #### 3) The original Jorgensen 1983 parameterization has no OH or HH 
+    #      lennard-jones interactions. For this behavior, uncomment these lines:
+    # pair_coeff  @atom:H @atom:H  lj/charmm/coul/charmm 0.00 0.4000
+    # pair_coeff  @atom:O @atom:H lj/charmm/coul/charmm  0.00 1.7753
+    #########################################################################
+
+    # Define a group for the tip3p water molecules:
+    group tip3p type  @atom:O  @atom:H
+
+    # Optional: Constrain the angles and distances.
+    #           (Most implementations use this, but it is optional.)
+    fix fSHAKE tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH
+    # (Remember to "unfix" fSHAKE during minimization.)
+
+  }
+
+} # "TIP3Pcharmm" water molecule type
+

tools/moltemplate/common/trappe1998.lt

@@ -0,0 +1,50 @@
+# This file stores complete LAMMPS data for the TraPPE model of saturated
+# hydrocarbon chains.  In this "united-atom" model, each methyl group is 
+# represented by a single atom.  Forces between "atoms" are taken from the 
+# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577)
+
+TraPPE {
+
+  write_once("In Init") {
+    # -- Default styles for "TraPPE" --
+    units           real
+    atom_style      full
+    # (Hybrid force field styles were used for portability.)
+    bond_style      hybrid harmonic
+    angle_style     hybrid harmonic
+    dihedral_style  hybrid opls
+    improper_style  none
+    pair_style      hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0
+    pair_modify     mix arithmetic
+    special_bonds   lj 0.0 0.0 0.0
+  }
+
+  write_once("Data Masses") {
+    @atom:CH2 14.1707
+    @atom:CH3 15.2507
+    @atom:CH4 16.3307
+  }
+
+  write_once("Data Angles By Type") {
+    @angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated
+  }
+
+  write_once("Data Dihedrals By Type") {
+    @dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated
+  }
+
+  write_once("In Settings") {
+    pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95
+    pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75
+    pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73
+    bond_coeff     @bond:saturated    harmonic   120.0   1.54
+    angle_coeff    @angle:backbone    harmonic   62.0022 114
+    dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0
+  }
+
+  write_once("In Settings") {
+    group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4
+  }
+
+}  # class TraPPE
+

tools/moltemplate/common/watmw.lt

@@ -0,0 +1,54 @@
+# This file stores LAMMPS data for the "mW" water model.
+# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016)
+#
+# In this model, each water molecule is represented by a single "mW" particle.
+# These particles interact with their neighbors via 3-body Stillinger-Weber 
+# forces whose parameters are tuned to mimic directional hydrogen-bonding
+# in liquid water (as well as hexagonal ice, type II ice, and
+# low-density super-cooled liquid/amorphous water phases).
+
+WatMW {
+  write("Data Atoms") {
+    $atom:mW $mol:. @atom:mW 0.0  0.0 0.0 0.0
+  }
+
+  write_once("Data Masses") {
+    @atom:mW 18.02
+  }
+
+  write_once("system.in.sw") {
+  mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0
+  }
+
+  write_once("In Init") {
+    # -- Default styles for "WatMW" --
+    units           real
+    pair_style      sw
+  }
+
+  write_once("In Settings") {
+    # --Now indicate which atom type(s) are simulated using the "sw" pair style 
+    # -- In this case only one of the atom types is used (the mW water "atom").
+
+    pair_coeff    * * sw system.in.sw mW NULL NULL NULL
+
+    # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so
+    # -- the atoms are identified by order in the list, not by name.  (The "mW" 
+    # -- refers to to an identifier in the system.in.sw file, not watmw.lt.)
+    # -- This command says that the first atom type corresponds to the "mW"
+    # -- atom in system.in.sw, and to ignore the remaining three atom types
+    # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt.
+    # --  We don't want to use the "sw" force field for interactions involving 
+    # --  these atom types, so we put "NULL" there.)
+    # -- Note: For this to work, you should probably run moltemplate this way:
+    # --     moltemplate.sh -a "@atom:WatMW/mW 1" system.lt
+    # -- This assigns the atom type named @atom:WatMW/mW to 1  (the first atom)
+  }
+
+  # -- optional --
+
+  write_once("In Settings") {
+    group WatMW type @atom:mW  #(Atoms of this type belong to the "WatMW" group)
+  }
+
+} # WatMW

tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT

@@ -0,0 +1,70 @@
+ This example shows how to put a protein (inclusion) in a 
+ lipid bilayer mixture composed of two different lipids (DPPC and DLPC).
+ The DPPC lipid model is described here:
+      G. Brannigan, P.F. Philips, and F.L.H. Brown,
+      Physical Review E, Vol 72, 011915 (2005)
+ (The DLPC model is a truncated version of DPPC. Modifications discussed below.)
+ The protein model is described here:
+      G. Bellesia, AI Jewett, and J-E Shea, 
+      Protein Science, Vol19 141-154 (2010)
+
+--- PREREQUISITES: ---
+
+1) This example requires the "dihedral_style fourier", which is currently 
+in the USER-MISC package.  Build LAMMPS with this package enabled using
+   make yes-user-misc
+before compiling LAMMPS. 
+(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.)
+
+2) This example may require additional features to be added to LAMMPS.
+If LAMMPS complains about an "Invalid pair_style", then
+ a) download the "additional_lammps_code" from 
+    http://moltemplate.org     (upper-left corner menu)
+ b) unpack it
+ c) copy the .cpp and .h files to the src folding of your lammps installation.
+ d) (re)compile LAMMPS.
+
+
+----- Details --------
+
+This example contains a coarse-grained model of a 4-helix bundle protein
+inserted into a lipid bilayer (made from a mixture of DPPC and DLPC).
+
+    -- Protein Model: --
+
+The coarse-grained protein is described in:
+   G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010)
+Here we use the "AUF2" model described in that paper.
+(The hydrophobic beads face outwards.)
+
+    -- Memebrane Model: --
+
+The DPPC lipid bilayer described in:
+     G. Brannigan, P.F. Philips, and F.L.H. Brown,
+     Physical Review E, Vol 72, 011915 (2005)
+and:
+     M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
+     J. Chem. Phys. 135, 244701 (2011)
+
+As in Watson(JCP 2011), rigid bond-length constraints 
+have been replaced by harmonic bonds. 
+
+A truncated version of this lipid (named "DLPC") has also been added. 
+The bending stiffness of each lipid has been increased to compensate 
+for the additional disorder resulting from mixing two different types 
+of lipids together.  (Otherwise pores appear.)
+Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models 
+have not been carefully parameterized to reproduce the correct behavior in 
+a lipid bilayer mixture.
+
+
+-------------
+
+Instructions on how to build LAMMPS input files and 
+run a short simulation are provided in other README files.
+
+step 1)
+README_setup.sh
+
+step2)
+README_run.sh

tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh

@@ -0,0 +1,33 @@
+# --- Running LAMMPS ---
+#  -- Prerequisites: --
+# The "run.in.nvt" file is a LAMMPS input script containing
+# references to the input scripts and data files
+# you hopefully have created earlier with moltemplate.sh:
+#   system.in.init, system.in.settings, system.data, and table_int.dat
+# If not, carry out the instructions in "README_setup.sh".
+#
+#  -- Instructions: --
+# If "lmp_linux" is the name of the command you use to invoke lammps,
+# then you would run lammps on these files this way:
+
+
+lmp_linux -i run.in.npt  # Run a simulation at constant pressure (tension)
+
+#or 
+
+lmp_linux -i run.in.nvt  # Run a simulation at constant volume
+
+#(Note: The constant volume simulation lacks pressure equilibration. These are
+#       completely separate simulations. The results of the constant pressure
+#       simulation are ignored when beginning the simulation at constant volume.
+#       This can be fixed.  Read "run.in.nvt" for equilibration instructions.)
+
+
+
+
+
+# If you have compiled the MPI version of lammps, you can run lammps in parallel
+#mpirun -np 4 lmp_linux -i run.in.npt
+#or
+#mpirun -np 4 lmp_linux -i run.in.nvt
+# (assuming you have 4 processors available)

tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh

@@ -0,0 +1,28 @@
+# Use these commands to generate the LAMMPS input script and data file
+# (and other auxilliary files):
+
+
+# Create LAMMPS input files this way:
+cd moltemplate_files
+
+  # run moltemplate
+
+  moltemplate.sh system.lt
+
+  # This will generate various files with names ending in *.in* and *.data. 
+  # These files are the input files directly read by LAMMPS.  Move them to 
+  # the parent directory (or wherever you plan to run the simulation).
+
+  mv -f system.in* system.data ../
+
+  # The "table_int.dat" file contains tabular data for the lipid INT-INT atom 
+  # 1/r^2 interaction.  We need it too. (This slows down the simulation by x2,
+  # so I might look for a way to get rid of it later.)
+  cp -f table_int.dat ../
+
+  # Optional:
+  # The "./output_ttree/" directory is full of temporary files generated by 
+  # moltemplate.  They can be useful for debugging, but are usually thrown away.
+  rm -rf output_ttree/
+
+cd ../

tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt

@@ -0,0 +1,87 @@
+
+ ------- To view a lammps trajectory in VMD --------
+
+
+1) Build a PSF file for use in viewing with VMD.
+
+This step works with VMD 1.9 and topotools 1.2.  
+(Older versions, like VMD 1.8.6, don't support this.)
+
+
+a) Start VMD
+b) Menu  Extensions->Tk Console
+c) Enter:
+
+(I assume that the the DATA file is called "system.data")
+
+   topo readlammpsdata system.data full
+   animate write psf system.psf
+
+2) 
+
+Later, to Load a trajectory in VMD:
+
+  Start VMD
+  Select menu: File->New Molecule
+ -Browse to select the PSF file you created above, and load it.
+  (Don't close the window yet.)
+ -Browse to select the trajectory file.
+  If necessary, for "file type" select: "LAMMPS Trajectory"
+  Load it.
+
+   ----  A note on trajectory format: -----
+If the trajectory is a DUMP file, then make sure the it contains the
+information you need for pbctools (see below.  I've been using this 
+command in my LAMMPS scripts to create the trajectories:
+
+  dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
+
+It's a good idea to use an atom_style which supports molecule-ID numbers 
+so that you can assign a molecule-ID number to each atom.  (I think this 
+is needed to wrap atom coordinates without breaking molecules in half.)
+
+Of course, you don't have to save your trajectories in DUMP format, 
+(other formats like DCD work fine)  I just mention dump files 
+because these are the files I'm familiar with.
+
+3) -----  Wrap the coordinates to the unit cell
+          (without cutting the molecules in half)
+
+a) Start VMD
+b) Load the trajectory in VMD (see above)
+c) Menu  Extensions->Tk Console
+d) Try entering these commands:
+
+    pbc wrap -compound res -all
+    pbc box
+
+    ----- Optional ----
+    Sometimes the solvent or membrane obscures the view of the solute.
+    It can help to shift the location of the periodic boundary box 
+    To shift the box in the y direction (for example) do this:
+
+    pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
+    pbc box -shiftcenterrel {0.0 0.15 0.0}
+
+    Distances are measured in units of box-length fractions, not Angstroms.
+
+    Alternately if you have a solute whose atoms are all of type 1, 
+    then you can also try this to center the box around it:
+
+    pbc wrap -sel type=1 -all -centersel type=2 -center com
+
+4) 
+    You should check if your periodic boundary conditions are too small.
+    To do that:
+       select Graphics->Representations menu option
+       click on the "Periodic" tab, and 
+       click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
+
+5) Optional: If you like, change the atom types in the PSF file so 
+   that VMD recognizes the atom types, use something like:
+
+sed -e 's/   1    1      /   C    C      /g' < system.psf > temp1.psf
+sed -e 's/   2    2      /   H    H      /g' < temp1.psf  > temp2.psf
+sed -e 's/   3    3      /   P    P      /g' < temp2.psf  > system.psf
+
+(If you do this, it might effect step 2 above.)

tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt

@@ -0,0 +1,254 @@
+# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in
+#      G. Bellesia, AI Jewett, and J-E Shea, 
+#      Protein Science, Vol19 141-154 (2010)
+#
+# Strategy:
+#
+#1) First I'll define some building blocks (A16, B16, T3)
+#   which are helices, sheets and turns of a predetermined length)
+#
+#2)  Then I'll copy and paste them together to build
+#    a 4-helix bundle (or a 4-strand beta-barrel).
+#    This approach is optional.  If your protein has helices which are not
+#    identical, you should probably just include all 4 helices in a single
+#    "Data Atoms" section and don't try to subdivide the protein into pieces.)
+
+
+
+1beadProtSci2010 {  # <-- enclose definitions in a namespace for portability
+
+  # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each)
+
+  A16 {
+
+    #  AtomID   MoleculeID AtomType  Charge       X        Y         Z
+
+    write('Data Atoms') {
+      $atom:a1  $mol:... @atom:../sL  0.0      -2.4      -2.4       0.0
+      $atom:a2  $mol:... @atom:../sL  0.0       2.4      -2.4       3.6
+      $atom:a3  $mol:... @atom:../sH  0.0       2.4       2.4       7.2
+      $atom:a4  $mol:... @atom:../sH  0.0      -2.4       2.4       10.8
+      $atom:a5  $mol:... @atom:../sL  0.0      -2.4      -2.4       14.4
+      $atom:a6  $mol:... @atom:../sL  0.0       2.4      -2.4       18.0
+      $atom:a7  $mol:... @atom:../sH  0.0       2.4       2.4       21.6
+      $atom:a8  $mol:... @atom:../sH  0.0      -2.4       2.4       25.2
+      $atom:a9  $mol:... @atom:../sL  0.0      -2.4      -2.4       28.8
+      $atom:a10 $mol:... @atom:../sL  0.0       2.4      -2.4       32.4
+      $atom:a11 $mol:... @atom:../sH  0.0       2.4       2.4       36.0
+      $atom:a12 $mol:... @atom:../sH  0.0      -2.4       2.4       39.6
+      $atom:a13 $mol:... @atom:../sL  0.0      -2.4      -2.4       43.2
+      $atom:a14 $mol:... @atom:../sL  0.0       2.4      -2.4       46.8
+      $atom:a15 $mol:... @atom:../sH  0.0       2.4       2.4       50.4
+      $atom:a16 $mol:... @atom:../sH  0.0      -2.4       2.4       54.0
+    }
+
+    write('Data Bonds') {
+      $bond:b1 @bond:../backbone $atom:a1 $atom:a2
+      $bond:b2 @bond:../backbone $atom:a2 $atom:a3
+      $bond:b3 @bond:../backbone $atom:a3 $atom:a4
+      $bond:b4 @bond:../backbone $atom:a4 $atom:a5
+      $bond:b5 @bond:../backbone $atom:a5 $atom:a6
+      $bond:b6 @bond:../backbone $atom:a6 $atom:a7
+      $bond:b7 @bond:../backbone $atom:a7 $atom:a8
+      $bond:b8 @bond:../backbone $atom:a8 $atom:a9
+      $bond:b9 @bond:../backbone $atom:a9 $atom:a10
+      $bond:b10 @bond:../backbone $atom:a10 $atom:a11
+      $bond:b11 @bond:../backbone $atom:a11 $atom:a12
+      $bond:b12 @bond:../backbone $atom:a12 $atom:a13
+      $bond:b13 @bond:../backbone $atom:a13 $atom:a14
+      $bond:b14 @bond:../backbone $atom:a14 $atom:a15
+      $bond:b15 @bond:../backbone $atom:a15 $atom:a16
+    }
+
+  } # A16
+
+
+  T3 { # T3 is a "turn" region consisting of 3 beads
+
+    #  AtomID   MoleculeID AtomType  Charge       X        Y         Z
+
+    write('Data Atoms') {
+      $atom:a1  $mol:... @atom:../tN  0.0      -4.8       0.0       0.0
+      $atom:a2  $mol:... @atom:../tN  0.0       0.0       3.3     -1.44
+      $atom:a3  $mol:... @atom:../tN  0.0       4.8       0.0       0.0
+    }
+
+    write('Data Bonds') {
+      $bond:b1 @bond:../backbone $atom:a1 $atom:a2
+      $bond:b2 @bond:../backbone $atom:a2 $atom:a3
+    }
+
+  } # T3
+
+
+  # ----- Now build a larger molecule using A16 and T3 -------
+
+  # Create a 4-Helix bundle.
+  # In this version, the hydrophobic beads are poing outward.
+  # I oriented them this way because I want to place this protein in a membrane.
+  # (There is another file in this directory containing alternate version
+  #  of this same molecule with the hydrophobic beads pointing inward.)
+
+  4HelixInsideOut {
+    helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4)
+    helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8)
+    helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2)
+    helix4 = new A16.rot(  45, 0,0,1).move(-5.70, 5.70,-21.6)
+
+    turn1  = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9)
+    turn2  = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0)
+    turn3  = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2)
+
+    write('Data Bonds') {
+      $bond:turn1a  @bond:../backbone   $atom:turn1/a1   $atom:helix1/a16
+      $bond:turn1b  @bond:../backbone   $atom:turn1/a3   $atom:helix2/a16
+      $bond:turn2a  @bond:../backbone   $atom:turn2/a1   $atom:helix3/a1
+      $bond:turn2b  @bond:../backbone   $atom:turn2/a3   $atom:helix2/a1
+      $bond:turn3a  @bond:../backbone   $atom:turn3/a1   $atom:helix3/a16
+      $bond:turn3b  @bond:../backbone   $atom:turn3/a3   $atom:helix4/a16
+    }
+    create_var { $mol } # molecule ID number shared by all atoms in this protein
+
+  } # 4HelixInsideOut
+
+
+  # -------- Minor coordinates adjustment: -----------
+
+  # Those coordinates in the commands above are a little too large.
+  # To make it easier to type them in, I was using sigma=6.0 Angstroms.
+  # Instead, here I'll try using sigma=5.5 Angstroms.   5.5/6 = 0.916667)
+
+  4HelixInsideOut.scale(0.9166666666666666)
+
+  # Note: "scale()" only effects the initial coordinates of
+  #       the molecule, not the force field parameters.
+  #       (If you plan to minimize the molecule, you don't need to 
+  #        be so careful about the initial coordinates.  In that case,
+  #        you don't have worry about "scale()".  Feel free to remove.)
+
+
+
+  #  -------------- Force-Field Parameters ------------
+
+  #  Units and force-field styles for this protein model
+  #  (These can be overridden later.)
+
+  write_once("In Init") {
+    units           real
+    atom_style      full
+    bond_style      hybrid harmonic
+    angle_style     hybrid harmonic
+    dihedral_style  hybrid fourier
+    pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0
+    pair_modify     mix arithmetic
+    special_bonds   lj 0.0 0.0 1.0   #(turn on "1-4" interactions)
+  }
+
+  #  --- Distance Units ---
+  # In this version of the model, sigma (the bond-length 
+  # and particle diameter) is rounded to 5.5 Angstroms.
+  #
+  #  --- Energy & Temperature Units ---
+  #   In this protein model, "epsilon" represents the free energy 
+  # bonus for bringing two hydrophobic amino acids together.  
+  # Here I choose to set epsilon to 1.806551818181818 kCal/mole.
+  # This value was chosen so that a temperature of 300 Kelvin lies at 
+  # 0.33 epsilon, which is the unfolding temperature of the marginally stable 
+  # "ASF1" protein model from the Bellesia et al 2010 paper.
+  #   This choice insures that both the "ASF1" model from that paper,
+  # as well as the much more stable "AUF2" protein we use here (which
+  # unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin,
+  # in the bulk at least.  (However it's not clear that these energy
+  # parameters will work well for a protein in membrane.  Perhaps I'll
+  # run some tests and fine tune these parameters for this scenario.)
+
+
+  # 2-body (non-bonded) interactions:
+  #
+  #   Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
+  #
+  #              i       j            pairstylename            eps sig K L
+  #
+  write_once("In Settings") {
+    pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter  1.8065518 5.5 1 -1
+    pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter  1.8065518 5.5 1 0
+    pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter  1.8065518 5.5 1 0
+  }
+
+  # The exact value of the bond_coeff does not matter too much as long as 
+  # it is "stiff enough".  Here I use a softer bond spring than the one 
+  # used in the paper so that I can increase the time step.
+  # I also use a relatively soft spring to constrain the bond angles.
+
+  #   bond_coeff     bondType            bondstylename    k    r0
+
+  write_once("In Settings") {
+    bond_coeff @bond:1beadProtSci2010/backbone harmonic  10.0  5.5
+  }
+
+
+
+  # We use the same bond-angle forces whenever 
+  # there are 3 consecutively-bonded atoms:
+  #
+  # angleType       atomtypes1 2 3   bondtypes1 2
+
+  write_once("Data Angles By Type") {
+    @angle:backbone    @atom:*  @atom:*  @atom:*   @bond:*  @bond:*
+  }
+
+  #   angle_coeff  angleType  anglestylename   k   theta0
+  write_once("In Settings") {
+    angle_coeff @angle:backbone   harmonic   100.0  105.0
+  }
+
+
+
+
+  #   Dihedral interactions are also determined by atom-type name in this case.
+  # I chose atoms whose type-names begin with "t" to be "turn" atoms.
+  # Atoms whose type-names begin with "s" could be either helices or sheets.
+  # (In this case, helices.  In this example, we use the @dihedral:delta65_0 
+  #  parameters.  This corresponds to the "AUF2" model from the
+  #  Bellesia et. al 2010 paper.)
+
+  #   dihedralType         atomtypes1 2 3 4                  bondtypes1 2 3
+
+  write_once("Data Dihedrals By Type") {
+    @dihedral:delta65_0  @atom:s* @atom:s* @atom:s* @atom:s*   *  *  *
+
+    # If "tN" (turn) atoms are present, use the @dihedral:turn parameters
+
+    @dihedral:turn       @atom:tN @atom:*  @atom:*  @atom:*    *  *  *
+  }
+
+
+  # From the Bellesia et al 2010 paper:
+  #             for helices: U_{dih}(\phi) = 1.2*(cos(3\phi) + cos(\phi+\delta))
+  #               for turns: U_{dih}(\phi) = 0.2*cos(3\phi)
+  #
+  # General formula used for "dihedral_style fourier":
+  # U_{dih}(\phi) = \Sum_{i=1}^m  K_i [ 1.0 + cos(n_i \phi - d_i) ]
+  #
+  # Syntax:
+  #                dihedralType dihedralstyle m  K_1 n_1 d_1  K2 n_2 d_2 ...
+
+  write_once("In Settings") {
+    dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0
+    dihedral_coeff @dihedral:delta62_5 fourier 2 2.167862 3 0 2.167862 1 -62.5
+    dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0
+    dihedral_coeff @dihedral:turn      fourier 1 0.361310 3 0
+    # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon.
+  }
+
+
+  #  --- Mass Units ---
+  # Typical amino acids weigh approximately 110.0 grams/mole.  (Rounding down):
+  write_once("Data Masses") {
+    @atom:1beadProtSci2010/sH 100.0
+    @atom:1beadProtSci2010/sL 100.0
+    @atom:1beadProtSci2010/tN 100.0
+  }
+
+} # 1beadProtSci2010 (namespace)
+

tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt

@@ -0,0 +1,225 @@
+### THIS FILE IS OPTIONAL AND IS NOT NECESSARY.  IN THIS FILE, I DEFINED SOME ##
+### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE##
+#
+# This file defines a family of coarse-grained protein models used in:
+#      G. Bellesia, AI Jewett, and J-E Shea, 
+#      Protein Science, Vol19 141-154 (2010)
+#
+# Strategy:
+#
+#1) First I'll define some building blocks (A16, B16, T3)
+#   which are helices, sheets and turns of a predetermined length)
+
+import "1beadProtSci2010.lt"
+
+#   We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below
+#
+#2)  Then I'll copy and paste them together to build
+#    a 4-helix bundle or a 4-strand beta-barrel.
+
+
+1beadProtSci2010 {  #<-- Add new molecules to existing namespace defined earlier
+                    #  This way we don't have to start from scratch.  We can
+                    #  use all the atom types and angle settings defined earlier
+
+  # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each)
+
+  B16 {
+
+    #  AtomID   MoleculeID AtomType  Charge      X         Y         Z
+
+    write('Data Atoms') {
+      $atom:a1  $mol:... @atom:../sL  0.0      -1.8       0.0       0.0
+      $atom:a2  $mol:... @atom:../sH  0.0       1.8       0.0       4.8
+      $atom:a3  $mol:... @atom:../sL  0.0      -1.8       0.0       9.6
+      $atom:a4  $mol:... @atom:../sH  0.0       1.8       0.0       14.4
+      $atom:a5  $mol:... @atom:../sL  0.0      -1.8       0.0       19.2
+      $atom:a6  $mol:... @atom:../sH  0.0       1.8       0.0       24.0
+      $atom:a7  $mol:... @atom:../sL  0.0      -1.8       0.0       28.8
+      $atom:a8  $mol:... @atom:../sH  0.0       1.8       0.0       33.6
+      $atom:a9  $mol:... @atom:../sL  0.0      -1.8       0.0       38.4
+      $atom:a10 $mol:... @atom:../sH  0.0       1.8       0.0       43.2
+      $atom:a11 $mol:... @atom:../sL  0.0      -1.8       0.0       48.0
+      $atom:a12 $mol:... @atom:../sH  0.0       1.8       0.0       52.8
+      $atom:a13 $mol:... @atom:../sL  0.0      -1.8       0.0       57.6
+      $atom:a14 $mol:... @atom:../sH  0.0       1.8       0.0       62.4
+      $atom:a15 $mol:... @atom:../sL  0.0      -1.8       0.0       67.2
+      $atom:a16 $mol:... @atom:../sH  0.0       1.8       0.0       72.0
+    }
+
+    write('Data Bonds') {
+      $bond:b1 @bond:../backbone $atom:a1 $atom:a2
+      $bond:b2 @bond:../backbone $atom:a2 $atom:a3
+      $bond:b3 @bond:../backbone $atom:a3 $atom:a4
+      $bond:b4 @bond:../backbone $atom:a4 $atom:a5
+      $bond:b5 @bond:../backbone $atom:a5 $atom:a6
+      $bond:b6 @bond:../backbone $atom:a6 $atom:a7
+      $bond:b7 @bond:../backbone $atom:a7 $atom:a8
+      $bond:b8 @bond:../backbone $atom:a8 $atom:a9
+      $bond:b9 @bond:../backbone $atom:a9 $atom:a10
+      $bond:b10 @bond:../backbone $atom:a10 $atom:a11
+      $bond:b11 @bond:../backbone $atom:a11 $atom:a12
+      $bond:b12 @bond:../backbone $atom:a12 $atom:a13
+      $bond:b13 @bond:../backbone $atom:a13 $atom:a14
+      $bond:b14 @bond:../backbone $atom:a14 $atom:a15
+      $bond:b15 @bond:../backbone $atom:a15 $atom:a16
+    }
+
+  } # B16
+
+  # ----- Now build larger molecules using B16 and T3 -------
+
+
+  4SheetBarrel {
+    sheet1 = new B16.rot(  45, 0,0,1).move(-4.762203156,-4.762203156, -36.0)
+    sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0)
+    sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0)
+    sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0)
+
+    turn1  = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6)
+    turn2  = new T3.rot(  0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4)
+    turn3  = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6)
+
+    write('Data Bonds') {
+      $bond:turn1a  @bond:../backbone  $atom:turn1/a1    $atom:sheet1/a16
+      $bond:turn1b  @bond:../backbone  $atom:turn1/a3    $atom:sheet2/a16
+      $bond:turn2a  @bond:../backbone  $atom:turn2/a1    $atom:sheet3/a1
+      $bond:turn2b  @bond:../backbone  $atom:turn2/a3    $atom:sheet2/a1
+      $bond:turn3a  @bond:../backbone  $atom:turn3/a1    $atom:sheet3/a16
+      $bond:turn3b  @bond:../backbone  $atom:turn3/a3    $atom:sheet4/a16
+    }
+    create_var { $mol } # molecule ID number shared by all atoms in this protein
+  }
+
+
+  # Below I define several alternate conformations of the"4HelixBundleInsideOut"
+  # molecule I defined earlier in "1beadProtSci2010.lt".  Same molecule however.
+
+  4HelixBundle {
+    helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4)
+    helix2 = new A16.rot(  45, 0,0,1).move( 5.70,-5.70,-28.8)
+    helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2)
+    helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6)
+
+    write('Data Bonds') {
+      $bond:turn1a  @bond:../backbone  $atom:turn1/a1    $atom:helix1/a16
+      $bond:turn1b  @bond:../backbone  $atom:turn1/a3    $atom:helix2/a16
+      $bond:turn2a  @bond:../backbone  $atom:turn2/a1    $atom:helix3/a1
+      $bond:turn2b  @bond:../backbone  $atom:turn2/a3    $atom:helix2/a1
+      $bond:turn3a  @bond:../backbone  $atom:turn3/a1    $atom:helix3/a16
+      $bond:turn3b  @bond:../backbone  $atom:turn3/a3    $atom:helix4/a16
+    }
+
+    turn1  = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(  8,0,0,1).move(-3.6,-4.8,28.2)
+    turn2  = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9)
+    turn3  = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4)
+
+    create_var { $mol } # molecule ID number shared by all atoms in this protein
+
+  } # 4HelixBundle
+
+
+
+
+  #  ---  alternate conformations (same molecule) ----
+
+  # In the following version, the helices are oriented in a similar way, 
+  # but they are separated a little further away from eachother.
+
+  4HelixBundleLoose {
+
+    helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0)
+    helix2 = new A16.rot(  45, 0,0,1).move( 6.7347723,-6.7347723, -27.0)
+    helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0)
+    helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0)
+
+    turn1  = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4)
+    turn2  = new T3.rot(  0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8)
+    turn3  = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4)
+
+    write('Data Bonds') {
+      $bond:turn1a  @bond:../backbone  $atom:turn1/a1    $atom:helix1/a16
+      $bond:turn1b  @bond:../backbone  $atom:turn1/a3    $atom:helix2/a16
+      $bond:turn2a  @bond:../backbone  $atom:turn2/a1    $atom:helix3/a1
+      $bond:turn2b  @bond:../backbone  $atom:turn2/a3    $atom:helix2/a1
+      $bond:turn3a  @bond:../backbone  $atom:turn3/a1    $atom:helix3/a16
+      $bond:turn3b  @bond:../backbone  $atom:turn3/a3    $atom:helix4/a16
+    }
+    create_var { $mol } # molecule ID number shared by all atoms in this protein
+  }
+
+
+  # In following version, the helices are oriented in a similar way, 
+  # but they are separated a little further away from eachother.
+
+  4HelixInsideOutLoose {
+    helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0)
+    helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0)
+    helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0)
+    helix4 = new A16.rot(  45, 0,0,1).move(-6.7347723, 6.7347723, -27.0)
+
+    turn1  = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8)
+    turn2  = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2)
+    turn3  = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8)
+
+    write('Data Bonds') {
+      $bond:turn1a  @bond:../backbone   $atom:turn1/a1   $atom:helix1/a16
+      $bond:turn1b  @bond:../backbone   $atom:turn1/a3   $atom:helix2/a16
+      $bond:turn2a  @bond:../backbone   $atom:turn2/a1   $atom:helix3/a1
+      $bond:turn2b  @bond:../backbone   $atom:turn2/a3   $atom:helix2/a1
+      $bond:turn3a  @bond:../backbone   $atom:turn3/a1   $atom:helix3/a16
+      $bond:turn3b  @bond:../backbone   $atom:turn3/a3   $atom:helix4/a16
+    }
+    create_var { $mol } # molecule ID number shared by all atoms in this protein
+
+  } # 4HelixInsideOutLoose
+
+
+
+
+  # In the following version, the 4 helices are arranged next to each other,
+  # side-by-side, in a planar conformation (instead of a compact bundle).
+
+  4HelixPlanar {
+    helix1 = new A16.rot(-00, 0,0,1).move(0,    0, -27.0)
+    helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0)
+    helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0)
+    helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0)
+
+    turn1  = new T3.rot(180,1,0,0).rot(  0,0,0,1).move( 4.8, 0, 31.8)
+    turn2  = new T3.rot(  0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8)
+    turn3  = new T3.rot(180,1,0,0).rot(  0,0,0,1).move(34.6, 0, 31.8)
+
+    write('Data Bonds') {
+      $bond:turn1a  @bond:../backbone   $atom:turn1/a1   $atom:helix1/a16
+      $bond:turn1b  @bond:../backbone   $atom:turn1/a3   $atom:helix2/a16
+      $bond:turn2a  @bond:../backbone   $atom:turn2/a1   $atom:helix3/a1
+      $bond:turn2b  @bond:../backbone   $atom:turn2/a3   $atom:helix2/a1
+      $bond:turn3a  @bond:../backbone   $atom:turn3/a1   $atom:helix3/a16
+      $bond:turn3b  @bond:../backbone   $atom:turn3/a3   $atom:helix4/a16
+    }
+    create_var { $mol } # molecule ID number shared by all atoms in this protein
+
+  } # 4HelixPlanar
+
+
+  # -------- Minor coordinates adjustment: -----------
+  # Those coordinates in the commands above are a little too large.
+  # To make it easier to type them in, I was using sigma=6.0 Angstroms.
+  # Instead, here I'll try using sigma=5.5 Angstroms.   5.5/6 = 0.916667)
+
+  4SheetBarrel.scale(0.9166666666666666)
+  4HelixBundle.scale(0.9166666666666666)
+  4HelixBundleLoose.scale(0.9166666666666666)
+  4HelixInsideOutLoose.scale(0.9166666666666666)
+  4HelixPlanar.scale(0.9166666666666666)
+
+  # Note: "scale()" only effects the initial coordinates of
+  #       the molecule, not the force field parameters.
+  #       (If you plan to minimize the molecule, you don't need to 
+  #        be so careful about the initial coordinates.  In that case,
+  #        you don't have worry about "scale()".  Feel free to remove.)
+
+
+} # 1beadProtSci2010 (namespace)
+

tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt

@@ -0,0 +1,198 @@
+# Note:
+#
+#    This example may require additional features to be added to LAMMPS.  If
+# LAMMPS complains about an "Invalid pair_style", then download copy the
+# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS
+# "src" directory and recompile LAMMPS.
+#
+# -------- Description --------
+#
+# This example contains an implementation of the DPPC lipid bilayer described in
+#      G. Brannigan, P.F. Philips, and F.L.H. Brown,
+#      Physical Review E, Vol 72, 011915 (2005)
+# and:
+#      M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
+#      J. Chem. Phys. 135, 244701 (2011)
+#
+# As in Watson(JCP 2011), rigid bond-length constraints have been replaced 
+# by harmonic bonds.
+#
+#   A truncated version of this lipid (named "DLPC") has also been added.
+# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully
+# parameterized to reproduce the correct behavior in a lipid bilayer mixture.
+#
+#   Units:
+#
+# The "epsilon" parameter in their model is approximately 2.75 kJ/mole
+#     ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ)
+# The "sigma" parameter corresponds to 7.5 angstroms.
+
+
+CGLipidBr2005 {
+
+
+  write_once("In Init") {
+    # -- Default styles for "CGLipidBr2005" --
+    units           real
+    atom_style      full
+    # (Hybrid force field styles were used for portability.)
+    bond_style      hybrid harmonic
+
+    #angle_style     hybrid cosine/delta # <- used in the original article
+    angle_style     hybrid harmonic  # <- prevents unphysical acute angle turns
+    # Explanation:
+    # angle_style cosine/delta:  U(theta) = k*(1-cos(theta-theta0))
+    # angle_style     harmonic:  U(theta) = k*(theta-theta0)^2
+
+    dihedral_style  none
+    improper_style  none
+    pair_style  hybrid table linear 1130 &
+                lj/charmm/coul/charmm/inter es4k4l 14.5 15
+    pair_modify     mix arithmetic
+    special_bonds   lj 0.0 0.0 1.0   # turn off pairs if "less than 3 bonds"
+
+    neighbor 2.0 multi  # <- perhaps unnecessary
+    communicate multi   # <- perhaps unnecessary
+  }
+
+
+  DPPC {
+    write("Data Atoms") {
+      $atom:h  $mol:. @atom:head     0.0  0.00  0.00  33.75 # DPPC head atom
+      $atom:i  $mol:. @atom:../int   0.0 -1.00  0.00  26.25
+      $atom:t1 $mol:. @atom:../tail  0.0  1.00  0.00  18.75
+      $atom:t2 $mol:. @atom:../tail  0.0 -1.00  0.00  11.25
+      $atom:t3 $mol:. @atom:../tail  0.0  1.00  0.00   3.75
+    }
+    write("Data Bonds") {
+      $bond:b1    @bond:../backbone   $atom:h  $atom:i
+      $bond:b2    @bond:../backbone   $atom:i  $atom:t1
+      $bond:b3    @bond:../backbone   $atom:t1 $atom:t2
+      $bond:b4    @bond:../backbone   $atom:t2 $atom:t3
+    }
+    write("Data Angles") {
+      $angle:a1   @angle:../backbone  $atom:h   $atom:i   $atom:t1
+      $angle:a2   @angle:../backbone  $atom:i   $atom:t1  $atom:t2
+      $angle:a3   @angle:../backbone  $atom:t1  $atom:t2  $atom:t3
+    }
+
+    # Define properties of the local (lipid-specific) atom:head type atom:
+    write_once("Data Masses") {
+      @atom:head  200.0
+    }
+    write_once("In Settings") {
+      pair_coeff @atom:head @atom:head   lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+      pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+    }
+
+  } #DPPC
+
+
+  DLPC {
+    write("Data Atoms") {
+      $atom:h  $mol:. @atom:head     0.0  0.00  0.00  30.00 # DLPC head atom
+      $atom:i  $mol:. @atom:../int   0.0 -1.00  0.00  22.50
+      $atom:t1 $mol:. @atom:../tail  0.0  1.00  0.00  15.00
+      $atom:t2 $mol:. @atom:../tail  0.0 -1.00  0.00   7.50
+    }
+    write("Data Bonds") {
+      $bond:b1    @bond:../backbone   $atom:h  $atom:i
+      $bond:b2    @bond:../backbone   $atom:i  $atom:t1
+      $bond:b3    @bond:../backbone   $atom:t1 $atom:t2
+    }
+    write("Data Angles") {
+      $angle:a1   @angle:../backbone  $atom:h   $atom:i   $atom:t1
+      $angle:a2   @angle:../backbone  $atom:i   $atom:t1  $atom:t2
+    }
+    # Define properties of the local (lipid-specific) atom:head type atom:
+    write_once("Data Masses") {
+      @atom:head  200.0
+    }
+    write_once("In Settings") {
+      pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+      pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+    }
+  } #DLPC
+
+
+  # Particles and properties shared by all lipid types:
+
+  write_once("Data Masses") {
+    @atom:int     200.0
+    @atom:tail    200.0
+    @atom:head    200.0  #<- Default head type.  We may override it later.
+  }
+
+  write_once("In Settings") {
+    # -- Default settings/parameters for "CGLipidBr2005" --
+    # (Hybrid bond & angle styles were used for portability.)
+
+    #  As in Watson(JCP 2011), rigid bond-length constraints 
+    #  have been replaced by harmonic bonds.
+    #  The k_theta parameter should lie in between 5*epsilon and 10*epsilon.
+    bond_coeff   @bond:backbone   harmonic     116.847 7.5 #<--2*5000*eps/sig^2
+  }
+
+  write_once("In Settings") {
+    #  cosine/delta: U(theta) = k*(1-cos(theta-theta0))
+    #angle_coeff  @angle:backbone  cosine/delta  4.60086042   180 #<--  7*eps
+    #  harmonic: U(theta) = k*(theta-theta0)^2     not (k/2)*(theta-theta0)^2
+    angle_coeff  @angle:backbone  harmonic      9.85898661    180 #<-->30*eps
+  }
+  # I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper
+  # to attempt to compensate for the fact that here we are using a lipid
+  # mixture of DPPC and DLPC.  (The mixture of lipids introduces a great deal 
+  # of disorder into the bilayer which would not be present in a DPPC bilayer.
+  # This causes pores to form.  Increasing the angle stiffness prevents this.)
+
+  write_once("In Settings") {
+
+    # The interaction of "atom:int" with other "atom:int" atoms is given by
+    # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at 
+    # r=3*sigma.  This was implemented using pair_style table.
+    # Unfortunately, mixing lj/charmm and "table" pair styles in the same
+    # simulation is very inneficient.
+
+  pair_coeff @atom:int  @atom:int  table  table_int.dat  INT
+
+    # The interaction of tail beads with eachother is given by the formula below
+    # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules:
+    # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6),
+  pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
+  pair_coeff @atom:int  @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
+
+    # The interaction of head beads which all other beads is given by:
+    # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6),
+
+  pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+  pair_coeff @atom:int  @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+
+
+  }  # write_once("In Settings")
+
+  # Note: I divided epsilon by 4 to get "0.1643" because we are using the 
+  # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6)
+  # (The "es4k4l" coeffstyle is the default.) Using this convention makes it
+  # easier to mix this coarse-grained lipid model with other molecular models.
+
+
+
+} # CGLipidBr2005
+
+
+
+
+
+
+
+
+# Note: This example has not been optimized for speed.
+#
+# Unfortunately, using both lj/charmm and "table" pair styles in the same
+# simulation seems to be very inneficient.  (The simulation is twice as slow
+# as using only the "lj/charmm" pair styles for every pairwise interaction, 
+# ...and about 25% slower than using "table" for every pairwise interaction.
+# However the lennard-jones pair styles support mixing, so we use them to
+# make it easier to run these molecules with other molecules which don't use
+# pair_table.  I felt that portability was worth the extra 25% slow down.)
+

tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py

@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+
+# Calculate a table of pairwise energies and forces between "INT" atoms
+# in the lipid membrane model described in 
+#   Brannigan et al, Phys Rev E, 72, 011915 (2005)
+# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
+# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity)
+
+# The previous version included the repulsive core term
+def U(r, eps, sigma):
+    return eps*   (0.4*pow((sigma/r),12)  -  3.0*sigma*sigma/(r*r))
+def F(r, eps, sigma):
+    return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
+# We don't want to do that.  Instead compute the core repulsion using a
+# different pair_style and add the attractive term on top of it using the table.
+# This way it the core repulsion acts as a default interaction with other atom
+# types (using the new repulsive mixing rules).
+
+epsilon = 2.75/4.184 # kCal/mole
+sigma   = 7.5
+Rmin    = 0.02
+Rmax    = 22.6
+rcut    = 22.5
+N       = 1130
+
+for i in range(0,N):
+    r = Rmin + i*(Rmax-Rmin)/(N-1)
+    U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma)
+    F_r = F(r, epsilon, sigma)
+    if r > rcut:
+        U_r = 0.0
+        F_r = 0.0
+    print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
+

tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py

@@ -0,0 +1,70 @@
+#!/usr/bin/env python
+
+# Calculate a table of pairwise energies and forces between "INT" atoms
+# in the lipid membrane model described in 
+#   Brannigan et al, Phys Rev E, 72, 011915 (2005)
+# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
+# I realized later this is not what we want because although energy is conserved
+# all enrgies are shifted with respect to energies used in the Brannigan paper
+# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole).
+# (So don't use this.)
+
+# Calculate and print a
+
+def S(r, rc1, rc2, derivative=False):
+    """ 
+    Calculate the switching function S(r) which decays continuously
+    between 1 and 0 in the range from rc1 to rc2 (rc2>rc1):
+       S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3
+    I'm using the same smoothing/switching cutoff function used by the CHARMM
+    force-fields.  (I'm even using the same code to implement it, taken 
+    from lammps charmm/coul/charmm pair style, rewritten in python.)
+
+    """
+    assert(rc2>rc1)
+    rsq           = r*r
+    rc1sq         = rc1*rc1
+    rc2sq         = rc2*rc2
+    denom_lj_inv  = (1.0 / ((rc2sq-rc1sq)*
+                            (rc2sq-rc1sq)*
+                            (rc2sq-rc1sq)))
+    if rsq > rc2sq:
+        return 0.0
+    elif rsq < rc1sq:
+        if derivative:
+            return 0.0
+        else:
+            return 1.0
+    else:
+        rc2sq_minus_rsq    = (rc2sq - rsq)
+        rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq
+        if derivative:
+            return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv)
+        else:
+            return (rc2sq_minus_rsq_sq *
+                    (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv)
+
+
+def U(r, eps, sigma):
+    return eps*   (0.4*pow((sigma/r),12) -   3.0*sigma*sigma/(r*r))
+
+def F(r, eps, sigma):
+    return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
+
+epsilon = 2.75/4.184 # kCal/mole
+sigma   = 7.5
+Rmin    = 0.02
+Rmax    = 22.6
+Rc1     = 22.0
+Rc2     = 22.5
+N       = 1130
+
+for i in range(0,N):
+    r = Rmin + i*(Rmax-Rmin)/(N-1)
+    U_r = U(r, epsilon, sigma)
+    F_r = F(r, epsilon, sigma)
+    # Multiply U(r) & F(r) by the smoothing/switch function
+    U_r = U_r * S(r, Rc1, Rc2)
+    F_r = U_r * S(r, Rc1, Rc2, True)  +  F_r * S(r, Rc1, Rc2, False)
+    print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
+

tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt

@@ -0,0 +1,207 @@
+# Description:
+
+# This example shows how to put a protein (inclusion) in a 
+# lipid bilayer mixture composed of two different lipids (DPPC and DLPC).
+# The DPPC lipid model is described here:
+#      G. Brannigan, P.F. Philips, and F.L.H. Brown,
+#      Physical Review E, Vol 72, 011915 (2005)
+# The protein model is described here:
+#      G. Bellesia, AI Jewett, and J-E Shea, 
+#      Protein Science, Vol19 141-154 (2010)
+# The new DLPC model is a truncated version of DPPC, 
+# (Its behaviour has not been rigorously tested.)
+# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to 
+# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293
+
+# Note:
+#   This example may require additional features to be added to LAMMPS.
+# If LAMMPS complains about an "Invalid pair_style", then copy the code
+# in the "additional_lammps_code" directory into your LAMMPS "src" directory
+# and recompile LAMMPS.
+
+
+
+import "CGLipidBr2005.lt"
+
+using namespace CGLipidBr2005
+
+# The "= new random" syntax chooses one of several molecules at random
+
+lipids = new random([DPPC, DLPC], [0.5,0.5], 1234)    #"1234"=random_seed
+                    [13].move(7.5,    0,     0)
+                    [15].move(3.75, 6.49519, 0)  # <-- hexagonal lattice
+                     [2].rot(180, 1, 0, 0)       # <-- 2 monolayers
+
+# Move all the lipds up to the center of the box
+
+lipids[*][*][*].move(0,0,75.0)
+
+
+
+
+# Although this patch of lipids is not square or rectangular, (it looks 
+# like a parallelogram), this is no longer the case after rectangular
+# periodic boundary conditions are applied. (Check by visualising in VMD.)
+
+
+write_once("Data Boundary") {                                        
+  0        97.5         xlo xhi
+  0        97.42785792  ylo yhi
+  0        150.0        zlo zhi                                     
+}
+
+
+# A note on geometry:
+# We want to create a bilayer arranged in a hexagonal lattice consisting of
+#    15 rows     (each row is aligned with the x-axis)
+#    13 columns  (aligned at a 60 degree angle from the x axis)
+# The lattice spacing is 7.5 Angstroms.
+# When wrapped onto a rectangular box, the dimensions of the system are:
+#    13 * 7.5 Angstroms           in the X direction
+#    15 * 7.5*sqrt(3)/2 Angstroms in the Y direction
+
+
+
+
+
+
+
+# ------------------- protein inclusion ---------------------
+
+import "1beadProtSci2010.lt"
+
+using namespace 1beadProtSci2010
+
+protein = new 4HelixInsideOut
+
+protein.move(45.0, 25.98076211, 75.0)
+
+
+# Delete a hole in the membrane to create space for the protein.
+
+delete lipids[4][2][*]
+delete lipids[6][2][*]
+delete lipids[3-6][3][*]
+delete lipids[3-5][4][*]
+delete lipids[2-5][5][*]
+delete lipids[2][6][*]
+delete lipids[4][6][*]
+
+# Note: All atom types must include the full path (the name of
+# the namespace which defined them as well as the atom type name).
+# (This is because we are no longer inside that namespace.)
+
+
+write_once("In Settings") {
+
+  # -----------------------------------------------------------
+  # -------- interactions between protein and lipids ----------
+  # -----------------------------------------------------------
+
+  # Interactions between the protein and lipid atoms are usually
+  # determined by mixing rules.  (However this is not possible some 
+  # for atoms, such as the "int" atoms in the lipid model which 
+  # interact using -1/r^2 attraction.)  Mixing rules do not make
+  # sense for these atoms so we must explicitly define their 
+  # interaction with all other atoms.
+
+  # We want the hydrophobic interactions between hydrophobic residues in 
+  # the protein and beads the interior of the lipid to be energetically 
+  # similar to the attractive interactions between the lipid tails.
+  #
+  # Note: I made the width of the outward-facing protein beads slightly larger
+  # ("12.5") whenever they interact with the "tail" beads in each lipid
+  # (in order to make the protein wider there).
+  # This hopefully relieves some of the internal negative pressure in the center
+  # of the bilayer which can otherwise rip apart the protein or suck it into 
+  # the bilaer.  (This is a hack, and I'm not sure if it is necessary.
+  # For different protein or lipid models, you probably don't need this.)
+  #
+  #                  i                      j                   pairstylename                     eps   sig  K  L
+
+  pair_coeff @atom:CGLipidBr2005/tail      @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 12.5 0.4 -1
+  pair_coeff @atom:CGLipidBr2005/int       @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
+
+  # To help keep the protein from tilting 90 degrees and burying itself 
+  # within the lipid bilayer, we make the turn regions at either 
+  # end of the protein (strongly)  attracted to the head groups 
+  # of the lipid.  (In reality, they  would probably be attracted 
+  # to the water as well.)
+
+  pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
+  pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
+
+  # All other interactions between proteins and lipids are steric.
+
+  pair_coeff @atom:CGLipidBr2005/tail      @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+  pair_coeff @atom:CGLipidBr2005/tail      @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+
+  pair_coeff @atom:CGLipidBr2005/int       @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+  pair_coeff @atom:CGLipidBr2005/int       @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+
+  pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+  pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+
+  pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+  pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+
+
+  # -----------------------------------------------------------
+  # -------- Modifications to the protein model: --------------
+  # -----------------------------------------------------------
+  #
+  # Turn off attraction between the hydrophobic "@atom:sH" beads:
+  # (These beads are located in the outside of a trans-membrane protein.)
+
+  pair_coeff @atom:1beadProtSci2010/sH @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter  1.8065518 5.5 1 0
+
+  # (Why: These beads are only attracted to 
+  #       each other in an aqueous environment)
+
+  # ... and
+  # Turn ON attraction between the hydrophilic "@atom:sL" beads.
+  # (These beads are located in the interior of a trans-membrane protein.)
+
+  pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter  1.8065518 5.5 1 -1
+
+  # Why?
+  #   In reality, polar groups in the interior of trans-membrane 
+  # proteins do form hydrogen bonds with each other.  This was 
+  # absent from the original protein model because, in an aqueous 
+  # environment, these groups preferentially interact with the water.
+  #
+  # Why is this necessary?
+  #   Shouldn't attraction between lipid tails and the protein create
+  # an effective force which brings the hydrophilic beads together?
+  # (similar to the hydrophobic effect, but in reverse?).
+  # Answer:
+  #   Unlike an aqueous environment (~zero pressure, or +1atm), there is 
+  # a large negative pressure in the interior of some bilayer membrane 
+  # models (such as this one).  Without some kind of direct attraction 
+  # between interior residues, the protein will get pulled apart.
+  # (Perhaps the attractive force I am using is too strong?)
+
+}
+
+
+
+
+# Finally, we must combine the two force-field styles which were used for
+# the coarse-grained lipid and protein.  To do that, we write one last time 
+# to the "In Init" section.  When reading the "Init" section LAMMPS will 
+# read these commands last and this will override any earlier settings.
+
+write_once("In Init") {
+  # -- These styles override earlier settings --
+  units           real
+  atom_style      full
+  # (Hybrid force field styles were used for portability.)
+  bond_style      hybrid harmonic
+  angle_style     hybrid cosine/delta harmonic
+  dihedral_style  hybrid fourier
+  improper_style  none
+  pair_style  hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15
+  pair_modify     mix arithmetic
+  special_bonds   lj 0.0 0.0 1.0   # turn off pairs if "less than 3 bonds"
+}
+

tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.min

@@ -0,0 +1,35 @@
+# -------- REQUIREMENTS: ---------
+# 1) This example requires the "USER-MISC" package.  (Use "make yes-USER-MISC")
+#   http://lammps.sandia.gov/doc/Section_start.html#start_3
+# 2) It also may require additional features and bug fixes for LAMMPS.
+#   So, after typing "make yes-user-misc" in to the shell, ...
+#   be sure to download and copy the "additional_lammps_code" from 
+#   http://moltemplate.org     (upper-left corner menu)
+# 3) Unpack it
+# 4) copy the .cpp and .h files to the src folding of your lammps installation.
+# 5) Compile LAMMPS.
+#
+# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
+# then you made a mistake in the instructions above.
+
+
+
+# -- Init section --
+
+include system.in.init
+
+# -- Atom definition section --
+
+read_data system.data
+
+# -- Settings Section --
+
+include system.in.settings
+
+# -- Run section --
+
+dump            1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
+
+minimize 1.0e-5 1.0e-7 500 2000
+
+write_restart  system_after_min.rst

tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt

@@ -0,0 +1,60 @@
+# -------- REQUIREMENTS: ---------
+# 1) This example requires the "USER-MISC" package.  (Use "make yes-USER-MISC")
+#   http://lammps.sandia.gov/doc/Section_start.html#start_3
+# 2) It also may require additional features and bug fixes for LAMMPS.
+#   So, after typing "make yes-user-misc" in to the shell, ...
+#   be sure to download and copy the "additional_lammps_code" from 
+#   http://moltemplate.org     (upper-left corner menu)
+# 3) Unpack it
+# 4) copy the .cpp and .h files to the src folding of your lammps installation.
+# 5) Compile LAMMPS.
+#
+# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
+# then you made a mistake in the instructions above.
+#
+
+# -- Init Section --
+
+include system.in.init
+
+# -- Atom Definition Section --
+
+read_data system.data
+
+# -- Settings Section --
+
+include system.in.settings
+
+# -- Run Section --
+
+#minimize 1.0e-5 1.0e-7 500 2000
+
+timestep      10.0  # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
+dump          1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz
+
+
+thermo_style  custom step temp pe etotal vol epair ebond eangle
+thermo        1000  # time interval for printing out "thermo" data
+
+
+fix fxlan all langevin  300.0 300.0  120 48279
+fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy
+
+
+# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon
+#        (for the "epsilon" used by the coarse-grained lipid), and
+#       to 0.33*epsilon (for the "epsilon" used in the coarse-grained protein)
+# Note: The langevin damping parameter "120" corresponds to 
+#       the 0.12ps damping time used in Watson et. al JCP 2011.
+# Note: We maintain the system system at constant (zero) tention 
+#       using a barostat damping parameter Pdamp=1000 ("0 0 1000")
+
+
+# optional (not sure if this helps):
+# balance x uniform y uniform
+
+
+run           10000000
+
+write_restart system_after_npt.rst
+

tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt

@@ -0,0 +1,67 @@
+# -------- REQUIREMENTS: ---------
+# 1) This example requires the "USER-MISC" package.  (Use "make yes-USER-MISC")
+#   http://lammps.sandia.gov/doc/Section_start.html#start_3
+# 2) It also may require additional features and bug fixes for LAMMPS.
+#   So, after typing "make yes-user-misc" in to the shell, ...
+#   be sure to download and copy the "additional_lammps_code" from 
+#   http://moltemplate.org     (upper-left corner menu)
+# 3) Unpack it
+# 4) copy the .cpp and .h files to the src folding of your lammps installation.
+# 5) Compile LAMMPS.
+#
+# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
+# then you made a mistake in the instructions above.
+#
+# ------------------------------- Initialization Section --------------------
+
+include         system.in.init
+
+# ------------------------------- Atom Definition Section -------------------
+
+
+# Normally, I would minimize the system and equilibrate the system at constant
+# pressure and temperature beforehand.  If you run lammps with "run.in.npt",
+# it will generate a restart file "system_after_npt.rst" with reasonable
+# coordinates at that temperature and pressure.  Then we could load it now:
+#
+#read_restart    system_after_npt.rst
+#
+# Unfortunately the LAMMPS "read_restart" command has been undependable over
+# the past year (2012), and I feel it is safer to remove it from the examples.
+# Instead, for this example, I just read the raw coordinates generated by 
+# moltemplate (and the default volume).  (I get fewer questions this way.) 
+# However you should never run any liquid simulations at constant volume without
+# pressure equilibration first.  Hopefully in the future "read_restart" will
+# work.  Until then, try "read_dump", "dump2data.py", or "restart2data".
+
+read_data       system.data
+
+# ------------------------------- Settings Section --------------------------
+
+include         system.in.settings
+
+# ------------------------------- Run Section -------------------------------
+
+
+timestep      10.0  # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
+dump          1 all custom 10000 traj_nvt.lammpstrj id mol type x y z ix iy iz
+
+
+thermo_style  custom step temp pe etotal vol epair ebond eangle
+thermo        1000  # time interval for printing out "thermo" data
+
+
+fix fxlan all langevin 300.0 300.0 120 48279
+fix fxnve all nve
+
+# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB.
+#       So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon.
+# Note: The langevin damping parameter "120" corresponds to 
+#       the 0.12ps damping time used in Watson et. al JCP 2011.
+
+#restart       500000
+
+run           10000000
+
+write_restart system_after_nvt.rst
+

tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT

@@ -0,0 +1,33 @@
+Note:
+   This example may require additional features to be added to LAMMPS.
+If LAMMPS complains about an "Invalid pair_style", then copy the code
+in the "additional_lammps_code" directory into your LAMMPS "src" directory
+and recompile LAMMPS.
+
+----- Description --------
+
+This example contains an implementation of the DPPC lipid bilayer described in:
+     G. Brannigan, P.F. Philips, and F.L.H. Brown,
+     Physical Review E, Vol 72, 011915 (2005)
+and:
+     M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
+     J. Chem. Phys. 135, 244701 (2011)
+
+As in Watson(JCP 2011), rigid bond-length constraints 
+have been replaced by harmonic bonds. 
+
+A truncated version of this lipid (named "DLPC") has also been added.
+Unlike the original "DPPC" molecule model, "DLPC" has not been carefully
+parameterized to reproduce the correct behavior in a lipid bilayer mixture.
+
+
+-------------
+
+Instructions on how to build LAMMPS input files and 
+run a short simulation are provided in other README files.
+
+step 1)
+README_setup.sh
+
+step2)
+README_run.sh

tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh

@@ -0,0 +1,33 @@
+# --- Running LAMMPS ---
+#  -- Prerequisites: --
+# The "run.in.nvt" file is a LAMMPS input script containing
+# references to the input scripts and data files
+# you hopefully have created earlier with moltemplate.sh:
+#   system.in.init, system.in.settings, system.data, and table_int.dat
+# If not, carry out the instructions in "README_setup.sh".
+#
+#  -- Instructions: --
+# If "lmp_linux" is the name of the command you use to invoke lammps,
+# then you would run lammps on these files this way:
+
+
+lmp_linux -i run.in.npt  # Run a simulation at constant pressure (tension)
+
+#or 
+
+lmp_linux -i run.in.nvt  # Run a simulation at constant volume
+
+#(Note: The constant volume simulation lacks pressure equilibration. These are
+#       completely separate simulations. The results of the constant pressure
+#       simulation are ignored when beginning the simulation at constant volume.
+#       This can be fixed.  Read "run.in.nvt" for equilibration instructions.)
+
+
+
+
+
+# If you have compiled the MPI version of lammps, you can run lammps in parallel
+#mpirun -np 4 lmp_linux -i run.in.npt
+#or
+#mpirun -np 4 lmp_linux -i run.in.nvt
+# (assuming you have 4 processors available)

tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh

@@ -0,0 +1,28 @@
+# Use these commands to generate the LAMMPS input script and data file
+# (and other auxilliary files):
+
+
+# Create LAMMPS input files this way:
+cd moltemplate_files
+
+  # run moltemplate
+
+  moltemplate.sh system.lt
+
+  # This will generate various files with names ending in *.in* and *.data. 
+  # These files are the input files directly read by LAMMPS.  Move them to 
+  # the parent directory (or wherever you plan to run the simulation).
+
+  mv -f system.in* system.data ../
+
+  # The "table_int.dat" file contains tabular data for the lipid INT-INT atom 
+  # 1/r^2 interaction.  We need it too. (This slows down the simulation by x2,
+  # so I might look for a way to get rid of it later.)
+  cp -f table_int.dat ../
+
+  # Optional:
+  # The "./output_ttree/" directory is full of temporary files generated by 
+  # moltemplate.  They can be useful for debugging, but are usually thrown away.
+  rm -rf output_ttree/
+
+cd ../

tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt

@@ -0,0 +1,87 @@
+
+ ------- To view a lammps trajectory in VMD --------
+
+
+1) Build a PSF file for use in viewing with VMD.
+
+This step works with VMD 1.9 and topotools 1.2.  
+(Older versions, like VMD 1.8.6, don't support this.)
+
+
+a) Start VMD
+b) Menu  Extensions->Tk Console
+c) Enter:
+
+(I assume that the the DATA file is called "system.data")
+
+   topo readlammpsdata system.data full
+   animate write psf system.psf
+
+2) 
+
+Later, to Load a trajectory in VMD:
+
+  Start VMD
+  Select menu: File->New Molecule
+ -Browse to select the PSF file you created above, and load it.
+  (Don't close the window yet.)
+ -Browse to select the trajectory file.
+  If necessary, for "file type" select: "LAMMPS Trajectory"
+  Load it.
+
+   ----  A note on trajectory format: -----
+If the trajectory is a DUMP file, then make sure the it contains the
+information you need for pbctools (see below.  I've been using this 
+command in my LAMMPS scripts to create the trajectories:
+
+  dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
+
+It's a good idea to use an atom_style which supports molecule-ID numbers 
+so that you can assign a molecule-ID number to each atom.  (I think this 
+is needed to wrap atom coordinates without breaking molecules in half.)
+
+Of course, you don't have to save your trajectories in DUMP format, 
+(other formats like DCD work fine)  I just mention dump files 
+because these are the files I'm familiar with.
+
+3) -----  Wrap the coordinates to the unit cell
+          (without cutting the molecules in half)
+
+a) Start VMD
+b) Load the trajectory in VMD (see above)
+c) Menu  Extensions->Tk Console
+d) Try entering these commands:
+
+    pbc wrap -compound res -all
+    pbc box
+
+    ----- Optional ----
+    Sometimes the solvent or membrane obscures the view of the solute.
+    It can help to shift the location of the periodic boundary box 
+    To shift the box in the y direction (for example) do this:
+
+    pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
+    pbc box -shiftcenterrel {0.0 0.15 0.0}
+
+    Distances are measured in units of box-length fractions, not Angstroms.
+
+    Alternately if you have a solute whose atoms are all of type 1, 
+    then you can also try this to center the box around it:
+
+    pbc wrap -sel type=1 -all -centersel type=2 -center com
+
+4) 
+    You should check if your periodic boundary conditions are too small.
+    To do that:
+       select Graphics->Representations menu option
+       click on the "Periodic" tab, and 
+       click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
+
+5) Optional: If you like, change the atom types in the PSF file so 
+   that VMD recognizes the atom types, use something like:
+
+sed -e 's/   1    1      /   C    C      /g' < system.psf > temp1.psf
+sed -e 's/   2    2      /   H    H      /g' < temp1.psf  > temp2.psf
+sed -e 's/   3    3      /   P    P      /g' < temp2.psf  > system.psf
+
+(If you do this, it might effect step 2 above.)

tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt

@@ -0,0 +1,191 @@
+# Note:
+#
+#    This example may require additional features to be added to LAMMPS.  If
+# LAMMPS complains about an "Invalid pair_style", then download copy the
+# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS
+# "src" directory and recompile LAMMPS.
+#
+# -------- Description --------
+#
+# This example contains an implementation of the DPPC lipid bilayer described in
+#      G. Brannigan, P.F. Philips, and F.L.H. Brown,
+#      Physical Review E, Vol 72, 011915 (2005)
+# and:
+#      M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
+#      J. Chem. Phys. 135, 244701 (2011)
+#
+# As in Watson(JCP 2011), rigid bond-length constraints have been replaced 
+# by harmonic bonds.
+#
+# --- DLPC lipids ---
+#   A truncated version of the DPPC lipid (named "DLPC") has also been added.
+# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully
+# parameterized to reproduce the correct behavior in a lipid bilayer/mixture.
+# (You may need to stiffen the bond-angle forces to make it behave correctly,
+#  but I did not do this here.)
+#
+#   Units:
+#
+# The "epsilon" parameter in their model is approximately 2.75 kJ/mole
+#     ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ)
+# The "sigma" parameter corresponds to 7.5 angstroms.
+#
+#
+# The new DLPC model is a truncated version of DPPC, 
+# (Its behaviour has not been rigorously tested.)
+
+
+CGLipidBr2005 {
+
+
+  write_once("In Init") {
+    # -- Default styles for "CGLipidBr2005" --
+    units           real
+    atom_style      full
+    # (Hybrid force field styles were used for portability.)
+    bond_style      hybrid harmonic
+    angle_style     hybrid cosine/delta
+    dihedral_style  none
+    improper_style  none
+    pair_style  hybrid table linear 1001 &
+                lj/charmm/coul/charmm/inter es4k4l 14.5 15
+    pair_modify     mix arithmetic
+    special_bonds   lj 0.0 0.0 1.0   # turn off pairs if "less than 3 bonds"
+
+    neighbor 2.0 multi  # <- perhaps unnecessary
+    communicate multi   # <- perhaps unnecessary
+  }
+
+
+  DPPC {
+    write("Data Atoms") {
+      $atom:h  $mol:. @atom:head     0.0  0.00  0.00  33.75 # DPPC head atom
+      $atom:i  $mol:. @atom:../int   0.0 -1.00  0.00  26.25
+      $atom:t1 $mol:. @atom:../tail  0.0  1.00  0.00  18.75
+      $atom:t2 $mol:. @atom:../tail  0.0 -1.00  0.00  11.25
+      $atom:t3 $mol:. @atom:../tail  0.0  1.00  0.00   3.75
+    }
+    write("Data Bonds") {
+      $bond:b1    @bond:../backbone   $atom:h  $atom:i
+      $bond:b2    @bond:../backbone   $atom:i  $atom:t1
+      $bond:b3    @bond:../backbone   $atom:t1 $atom:t2
+      $bond:b4    @bond:../backbone   $atom:t2 $atom:t3
+    }
+    write("Data Angles") {
+      $angle:a1   @angle:../backbone  $atom:h   $atom:i   $atom:t1
+      $angle:a2   @angle:../backbone  $atom:i   $atom:t1  $atom:t2
+      $angle:a3   @angle:../backbone  $atom:t1  $atom:t2  $atom:t3
+    }
+
+    # Define properties of the local (lipid-specific) atom:head type atom:
+    write_once("Data Masses") {
+      @atom:head  200.0
+    }
+    write_once("In Settings") {
+      pair_coeff @atom:head @atom:head   lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+      pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+    }
+
+  } #DPPC
+
+
+  DLPC {
+    write("Data Atoms") {
+      $atom:h  $mol:. @atom:head     0.0  0.00  0.00  30.00 # DLPC head atom
+      $atom:i  $mol:. @atom:../int   0.0 -1.00  0.00  22.50
+      $atom:t1 $mol:. @atom:../tail  0.0  1.00  0.00  15.00
+      $atom:t2 $mol:. @atom:../tail  0.0 -1.00  0.00   7.50
+    }
+    write("Data Bonds") {
+      $bond:b1    @bond:../backbone   $atom:h  $atom:i
+      $bond:b2    @bond:../backbone   $atom:i  $atom:t1
+      $bond:b3    @bond:../backbone   $atom:t1 $atom:t2
+    }
+    write("Data Angles") {
+      $angle:a1   @angle:../backbone  $atom:h   $atom:i   $atom:t1
+      $angle:a2   @angle:../backbone  $atom:i   $atom:t1  $atom:t2
+    }
+    # Define properties of the local (lipid-specific) atom:head type atom:
+    write_once("Data Masses") {
+      @atom:head  200.0
+    }
+    write_once("In Settings") {
+      pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+      pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+    }
+  } #DLPC
+
+
+  # Particles shared by all lipid types
+  write_once("Data Masses") {
+    @atom:int     200.0
+    @atom:tail    200.0
+    @atom:head    200.0  #<- Default head type.  We may override it later.
+  }
+
+  write_once("In Settings") {
+    # -- Default settings/parameters for "CGLipidBr2005" --
+    # (Hybrid bond & angle styles were used for portability.)
+
+    #  As in Watson(JCP 2011), rigid bond-length constraints 
+    #  have been replaced by harmonic bonds.
+    #  The k_theta parameter should lie in between 5*epsilon and 10*epsilon.
+    bond_coeff   @bond:backbone   harmonic     116.847 7.5 #<--2*5000*eps/sig^2
+  }
+
+  write_once("In Settings") {
+    angle_coeff  @angle:backbone  cosine/delta  4.60086042   180 #<--  7*eps
+    #angle_coeff  @angle:backbone  cosine/delta   6.57265774   180 #<-- 10*eps
+  }
+
+  write_once("In Settings") {
+
+    # The interaction of "atom:int" with other "atom:int" atoms is given by
+    # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at 
+    # r=3*sigma.  This was implemented using pair_style table.
+    # Unfortunately, mixing lj/charmm and "table" pair styles in the same
+    # simulation is very inneficient.
+
+  pair_coeff @atom:int  @atom:int  table  table_int.dat  INT
+
+    # The interaction of tail beads with eachother is given by the formula below
+    # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules:
+    # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6),
+  pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
+  pair_coeff @atom:int  @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
+
+    # The interaction of head beads which all other beads is given by:
+    # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6),
+
+  pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+  pair_coeff @atom:int  @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
+
+
+  }  # write_once("In Settings")
+
+  # Note: I divided epsilon by 4 to get "0.1643" because we are using the 
+  # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6)
+  # (The "es4k4l" coeffstyle is the default.) Using this convention makes it
+  # easier to mix this coarse-grained lipid model with other molecular models.
+
+
+
+} # CGLipidBr2005
+
+
+
+
+
+
+
+
+# Note: This example has not been optimized for speed.
+#
+# Unfortunately, using both lj/charmm and "table" pair styles in the same
+# simulation seems to be very inneficient.  (The simulation is twice as slow
+# as using only the "lj/charmm" pair styles for every pairwise interaction, 
+# ...and about 25% slower than using "table" for every pairwise interaction.
+# However the lennard-jones pair styles support mixing, so we use them to
+# make it easier to run these molecules with other molecules which don't use
+# pair_table.  I felt that portability was worth the extra 25% slow down.)
+

tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py

@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+
+# Calculate a table of pairwise energies and forces between "INT" atoms
+# in the lipid membrane model described in 
+#   Brannigan et al, Phys Rev E, 72, 011915 (2005)
+# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
+# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity)
+
+# The previous version included the repulsive core term
+def U(r, eps, sigma):
+    return eps*   (0.4*pow((sigma/r),12)  -  3.0*sigma*sigma/(r*r))
+def F(r, eps, sigma):
+    return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
+# We don't want to do that.  Instead compute the core repulsion using a
+# different pair_style and add the attractive term on top of it using the table.
+# This way it the core repulsion acts as a default interaction with other atom
+# types (using the new repulsive mixing rules).
+
+epsilon = 2.75/4.184 # kCal/mole
+sigma   = 7.5
+Rmin    = 0.02
+Rmax    = 22.6
+rcut    = 22.5
+N       = 1130
+
+for i in range(0,N):
+    r = Rmin + i*(Rmax-Rmin)/(N-1)
+    U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma)
+    F_r = F(r, epsilon, sigma)
+    if r > rcut:
+        U_r = 0.0
+        F_r = 0.0
+    print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
+

tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py

@@ -0,0 +1,70 @@
+#!/usr/bin/env python
+
+# Calculate a table of pairwise energies and forces between "INT" atoms
+# in the lipid membrane model described in 
+#   Brannigan et al, Phys Rev E, 72, 011915 (2005)
+# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
+# I realized later this is not what we want because although energy is conserved
+# all enrgies are shifted with respect to energies used in the Brannigan paper
+# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole).
+# (So don't use this.)
+
+# Calculate and print a
+
+def S(r, rc1, rc2, derivative=False):
+    """ 
+    Calculate the switching function S(r) which decays continuously
+    between 1 and 0 in the range from rc1 to rc2 (rc2>rc1):
+       S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3
+    I'm using the same smoothing/switching cutoff function used by the CHARMM
+    force-fields.  (I'm even using the same code to implement it, taken 
+    from lammps charmm/coul/charmm pair style, rewritten in python.)
+
+    """
+    assert(rc2>rc1)
+    rsq           = r*r
+    rc1sq         = rc1*rc1
+    rc2sq         = rc2*rc2
+    denom_lj_inv  = (1.0 / ((rc2sq-rc1sq)*
+                            (rc2sq-rc1sq)*
+                            (rc2sq-rc1sq)))
+    if rsq > rc2sq:
+        return 0.0
+    elif rsq < rc1sq:
+        if derivative:
+            return 0.0
+        else:
+            return 1.0
+    else:
+        rc2sq_minus_rsq    = (rc2sq - rsq)
+        rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq
+        if derivative:
+            return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv)
+        else:
+            return (rc2sq_minus_rsq_sq *
+                    (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv)
+
+
+def U(r, eps, sigma):
+    return eps*   (0.4*pow((sigma/r),12) -   3.0*sigma*sigma/(r*r))
+
+def F(r, eps, sigma):
+    return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
+
+epsilon = 2.75/4.184 # kCal/mole
+sigma   = 7.5
+Rmin    = 0.02
+Rmax    = 22.6
+Rc1     = 22.0
+Rc2     = 22.5
+N       = 1130
+
+for i in range(0,N):
+    r = Rmin + i*(Rmax-Rmin)/(N-1)
+    U_r = U(r, epsilon, sigma)
+    F_r = F(r, epsilon, sigma)
+    # Multiply U(r) & F(r) by the smoothing/switch function
+    U_r = U_r * S(r, Rc1, Rc2)
+    F_r = U_r * S(r, Rc1, Rc2, True)  +  F_r * S(r, Rc1, Rc2, False)
+    print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
+

tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt

@@ -0,0 +1,94 @@
+# Description:
+
+# This constructs a bilayer constructed from coarse-grained DPPC lipids
+# (implicit solvent).  The DPPC lipid model is described here:
+#      G. Brannigan, P.F. Philips, and F.L.H. Brown,
+#      Physical Review E, Vol 72, 011915 (2005)
+#
+# NOTE: There is an example of a 50%/50% DPPC & DLPC mixture
+#       in the "membrane+protein" and "vesicle" examples.
+
+
+
+
+
+
+import "CGLipidBr2005Orig.lt"
+
+using namespace CGLipidBr2005
+
+lipids = new DPPC  [32].move(7.5,    0,     0)
+                   [37].move(3.75, 6.49519, 0)
+                    [2].rot(180, 1, 0, 0)
+
+
+# Move the lipds up to the center of the box
+lipids[*][*][*].move(0,0,75.0)
+
+
+# Although this patch of lipids is not square or rectangular, (it looks 
+# like a parallelogram), this is no longer the case after rectangular
+# periodic boundary conditions are applied.  We apply them below:
+#   width:  240     = 32*7.5
+#   height: 240.322 = 37*6.49519
+
+write_once("Data Boundary") {                                        
+  0        240          xlo xhi
+  0        240.322      ylo yhi
+  0        150.0        zlo zhi                                     
+}
+
+
+
+
+
+
+
+
+# -------------- File ends here. Only comments below.-------------------
+
+# ------------------------------------
+# ------------- COMMENTS: ------------
+# ------------------------------------
+#
+# A note on geometry:
+# We want to create a bilayer arranged in a hexagonal lattice consisting of
+#    32 rows     (each row is aligned with the x-axis)
+#    37 columns  (aligned at a 60 degree angle from the x axis)
+# The lattice spacing is 8.0 Angstroms ( ~= 0.95*sigma*2^(1/6), where sigma=7.5)
+# When wrapped onto a rectangular box, the dimensions of the system are:
+#    32 * 7.5 Angstroms           in the X direction
+#    37 * 7.5*sqrt(3)/2 Angstroms in the Y direction
+# ------------------------------------
+#
+# Below I show simple ways to create a lipid bilayer:
+#
+# 1) If you just want to make lipid bilayer out of DPPC,
+#    without specifying the location of each lipid, you could use this syntax:
+#        lipids = new DPPC [32][37][2]   # 3-D array
+#    Later you can load in the coordinates of the lipds from a PDB file.
+#    Alternately you could also use a 1-dimensional array:
+#        lipids = new DPPC [2368]        # 1-D array.  Note: 2368 = 32 x 37 x 2
+#    It does not matter as long as the number of lipids is correct.
+#    Multidimensional arrays are only useful if you plan to apply independent
+#    coordinate transformations to each row and column and monolayer. See below:
+#
+# 2) Instead of loading a PDB file later, we can directly specify the location 
+#    of each DPPC lipid in the LT file itself.  For lipid bilayers, this is
+#    easy, because the bilayer structure resembles 2 planar lattices.
+#    We can use "move" commands to place each lipid, and the "rot" command
+#    to turn the lipids in one of the monolayers upside down.
+#    
+#        lipids = new DPPC [32].move(7.5,    0,     0)
+#                          [37].move(3.75, 6.49519, 0)
+#                           [2].rot(180, 1, 0, 0)
+#
+# 3) If you want to create a bilayer from a mixture of DPPC and DLPC, you must
+#   replace "DPPC" in the command above with random([DPPC,DLPC],[0.5,0.5],12345)
+#   Here "0.5,0.5" are the probabilities for each molecule type, and "12345"
+#   is an optional random seed.
+# lipids = new random([DPPC,DLPC], [0.5,0.5], 12345)
+#                    [32].move(7.5,    0,     0)
+#                    [37].move(3.75, 6.49519, 0)
+#                     [2].rot(180, 1, 0, 0)
+#

tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.min

@@ -0,0 +1,28 @@
+# -- Init section --
+
+include system.in.init
+
+# -- Atom definition section --
+
+read_data system.data
+
+# -- Settings Section --
+
+include system.in.settings
+
+# Optional: Make sure the pairwise energies look reasonable:
+#pair_write 2 2 1001 r 2.6 16.0 test_tail-tail.dat t-t 0 0
+#pair_write 2 3 1001 r 2.6 16.0 test_tail-head.dat t-h 0 0
+#pair_write 1 2 1001 r 2.6 16.0  test_int-tail.dat i-t 0 0
+#pair_write 1 1 2573 r 2.6 16.0   test_int-int.dat i-i 0 0
+#pair_write 1 3 1001 r 2.6 16.0  test_int-head.dat i-h 0 0
+#pair_write 3 3 1001 r 2.6 16.0  test_head-head.dat h-h 0 0
+
+
+# -- Run section --
+
+dump            1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
+
+minimize 1.0e-5 1.0e-7 500 2000
+
+write_restart  system_after_min.rst

tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt

@@ -0,0 +1,57 @@
+# -------- REQUIREMENTS: ---------
+# 1) This example may require additional features and bug fixes for LAMMPS.
+#   Be sure to download and copy the "additional_lammps_code" from 
+#   http://moltemplate.org     (upper-left corner menu)
+# 2) Unpack it
+# 3) copy the .cpp and .h files to the src folding of your lammps installation.
+# 4) Compile LAMMPS.
+#
+# (If LAMMPS complains about an "Invalid pair_style"
+#  then you made a mistake in the instructions above.)
+#
+
+# -- Init Section --
+
+include system.in.init
+
+# -- Atom Definition Section --
+
+read_data system.data
+
+# -- Settings Section --
+
+include system.in.settings
+
+# -- Run Section --
+
+
+timestep      6.0  # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
+dump          1 all custom 5000 traj_npt.lammpstrj id mol type x y z ix iy iz
+
+
+thermo_style  custom step temp pe etotal vol epair ebond eangle
+thermo        1000  # time interval for printing out "thermo" data
+
+
+fix fxlan all langevin  300.0 300.0  120 48279
+fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy
+
+
+# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon
+#       for the "epsilon" used by the coarse-grained lipid.
+# Note: The langevin damping parameter "120" corresponds to 
+#       the 0.12ps damping time used in Watson et. al JCP 2011.
+# Note: We maintain the system system at constant (zero) tention 
+#       using a barostat damping parameter Pdamp=1000 ("0 0 1000")
+
+
+# optional (not sure if this helps):
+# balance x uniform y uniform
+
+
+#restart      1000000
+
+run           2000000
+
+write_restart system_after_npt.rst
+

tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt

@@ -0,0 +1,53 @@
+# ------------------------------- Initialization Section --------------------
+
+include         system.in.init
+
+# ------------------------------- Atom Definition Section -------------------
+
+
+# Normally, I would minimize the system and equilibrate the system at constant
+# pressure and temperature beforehand.  If you run lammps with "run.in.npt",
+# it will generate a restart file "system_after_npt.rst" with reasonable
+# coordinates at that temperature and pressure.  Then we could load it now:
+#
+#read_restart    system_after_npt.rst
+#
+# Unfortunately the LAMMPS "read_restart" command has been undependable over
+# the past year (2012), and I feel it is safer to remove it from the examples.
+# Instead, for this example, I just read the raw coordinates generated by 
+# moltemplate (and the default volume).  (I get fewer questions this way.) 
+# However you should never run any liquid simulations at constant volume without
+# pressure equilibration first.  Hopefully in the future "read_restart" will
+# work.  Until then, try "read_dump", "dump2data.py", or "restart2data".
+
+read_data       system.data
+
+# ------------------------------- Settings Section --------------------------
+
+include         system.in.settings
+
+# ------------------------------- Run Section -------------------------------
+
+
+timestep      6.0  # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
+dump          1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz
+
+
+thermo_style  custom step temp pe etotal vol epair ebond eangle
+thermo        1000  # time interval for printing out "thermo" data
+
+
+fix fxlan all langevin 300.0 300.0 120 48279
+fix fxnve all nve
+
+# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB.
+#       So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon.
+# Note: The langevin damping parameter "120" corresponds to 
+#       the 0.12ps damping time used in Watson et. al JCP 2011.
+
+#restart       1000000
+
+run           1000000
+
+write_restart system_after_nvt.rst
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT

@@ -0,0 +1,33 @@
+# This directory contains examples of how to run a short simulation of a 
+# coarse-grained protein-like polymer, folding in the presence and absence of
+# a chaperone (modeled as an attractive or repulsie spherical shell).
+#
+# The protein models and the chaperone models are described and used here:
+# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
+# (http://www.pnas.org/content/101/36/13192)
+# ...and also here:
+# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006)
+#
+# (In the "frustrated+minichaperone" directory, the protein is 
+#  placed outside the chaperone sphere, as opposed to inside.)
+#
+# -------- REQUIREMENTS: ---------
+# 1) These examples require the "USER-MISC" package.  (Use "make yes-USER-MISC")
+#   http://lammps.sandia.gov/doc/Section_start.html#start_3
+# 2) They also may require additional features and bug fixes for LAMMPS.
+#   be sure to download and copy the "additional_lammps_code" from 
+#   http://moltemplate.org     (upper-left corner menu)
+# 3) Unpack it
+# 4) copy the .cpp and .h files to the src folding of your lammps installation.
+# 5) Compile LAMMPS.
+#
+
+-------------
+Instructions on how to build LAMMPS input files and 
+run a short simulation are provided in other README files in each directory.
+
+step 1)
+README_setup.sh
+
+step2)
+README_run.sh

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT

@@ -0,0 +1,32 @@
+# This directory demonstrates how to run a long simulation of 
+# the "frustrated" coarse-grained protein confined in a frustrated
+# coarse-grained chaperonin (R=6, h=0.475) as described in:
+# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
+# (http://www.pnas.org/content/101/36/13192)
+#
+# Note: If you want to use a "hydrophilic" chaperone (with h=0.0 
+#       instead of h=0.475), then replace the word "CHAP_INTERIOR_H0.475" 
+#       (at the end of "system.lt") with "CHAP_INTERIOR_H0"
+#
+# Because this process takes a long time (even with the help of the chaperone)
+# I save the data relatively infrequently.
+#
+# -------- REQUIREMENTS: ---------
+# 1) This example requires the "USER-MISC" package.  (Use "make yes-USER-MISC")
+#   http://lammps.sandia.gov/doc/Section_start.html#start_3
+# 2) It also may require additional features and bug fixes for LAMMPS.
+#   be sure to download and copy the "additional_lammps_code" from 
+#   http://moltemplate.org     (upper-left corner menu)
+# 3) Unpack it
+# 4) copy the .cpp and .h files to the src folding of your lammps installation.
+# 5) Compile LAMMPS.
+
+-------------
+Instructions on how to build LAMMPS input files and 
+run a short simulation are provided in other README files.
+
+step 1)
+README_setup.sh
+
+step2)
+README_run.sh

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh

@@ -0,0 +1,31 @@
+# You would probably run lammps this way:
+#
+# lmp_ubuntu -i run.in.nvt
+
+# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer
+# to the input scripts & data files you created earlier when you ran moltemplate
+# system.in.init, system.in.settings, system.data
+
+
+
+
+# -----------------------------------
+
+
+
+LAMMPS_COMMAND="lmp_ubuntu"
+
+# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
+# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary.
+
+# Run lammps using the following 3 commands:
+
+"$LAMMPS_COMMAND" -i run.in.min    # minimize         (OPTIONAL)
+"$LAMMPS_COMMAND" -i run.in.nvt    # production run
+
+# Alternately, if you have MPI installed, try something like this:
+
+#NUMPROCS=4
+#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min    # minimize  (OPTIONAL)
+#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt    # production run
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh

@@ -0,0 +1,24 @@
+# Use these commands to generate the LAMMPS input script and data file
+# (and other auxilliary files):
+
+
+# Create LAMMPS input files this way:
+cd moltemplate_files
+
+  # run moltemplate
+
+  moltemplate.sh -overlay-dihdedrals system.lt
+
+  # This will generate various files with names ending in *.in* and *.data. 
+  # These files are the input files directly read by LAMMPS.  Move them to 
+  # the parent directory (or wherever you plan to run the simulation).
+
+  mv -f system.in* system.data ../
+  cp -r table*.dat ../
+
+  # Optional:
+  # The "./output_ttree/" directory is full of temporary files generated by 
+  # moltemplate.  They can be useful for debugging, but are usually thrown away.
+  rm -rf output_ttree/
+
+cd ../

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt

@@ -0,0 +1,87 @@
+
+ ------- To view a lammps trajectory in VMD --------
+
+
+1) Build a PSF file for use in viewing with VMD.
+
+This step works with VMD 1.9 and topotools 1.2.  
+(Older versions, like VMD 1.8.6, don't support this.)
+
+
+a) Start VMD
+b) Menu  Extensions->Tk Console
+c) Enter:
+
+(I assume that the the DATA file is called "system.data")
+
+   topo readlammpsdata system.data full
+   animate write psf system.psf
+
+2) 
+
+Later, to Load a trajectory in VMD:
+
+  Start VMD
+  Select menu: File->New Molecule
+ -Browse to select the PSF file you created above, and load it.
+  (Don't close the window yet.)
+ -Browse to select the trajectory file.
+  If necessary, for "file type" select: "LAMMPS Trajectory"
+  Load it.
+
+   ----  A note on trajectory format: -----
+If the trajectory is a DUMP file, then make sure the it contains the
+information you need for pbctools (see below.  I've been using this 
+command in my LAMMPS scripts to create the trajectories:
+
+  dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
+
+It's a good idea to use an atom_style which supports molecule-ID numbers 
+so that you can assign a molecule-ID number to each atom.  (I think this 
+is needed to wrap atom coordinates without breaking molecules in half.)
+
+Of course, you don't have to save your trajectories in DUMP format, 
+(other formats like DCD work fine)  I just mention dump files 
+because these are the files I'm familiar with.
+
+3) -----  Wrap the coordinates to the unit cell
+          (without cutting the molecules in half)
+
+a) Start VMD
+b) Load the trajectory in VMD (see above)
+c) Menu  Extensions->Tk Console
+d) Try entering these commands:
+
+    pbc wrap -compound res -all
+    pbc box
+
+    ----- Optional ----
+    Sometimes the solvent or membrane obscures the view of the solute.
+    It can help to shift the location of the periodic boundary box 
+    To shift the box in the y direction (for example) do this:
+
+    pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
+    pbc box -shiftcenterrel {0.0 0.15 0.0}
+
+    Distances are measured in units of box-length fractions, not Angstroms.
+
+    Alternately if you have a solute whose atoms are all of type 1, 
+    then you can also try this to center the box around it:
+
+    pbc wrap -sel type=1 -all -centersel type=2 -center com
+
+4) 
+    You should check if your periodic boundary conditions are too small.
+    To do that:
+       select Graphics->Representations menu option
+       click on the "Periodic" tab, and 
+       click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
+
+5) Optional: If you like, change the atom types in the PSF file so 
+   that VMD recognizes the atom types, use something like:
+
+sed -e 's/   1    1      /   C    C      /g' < system.psf > temp1.psf
+sed -e 's/   2    2      /   H    H      /g' < temp1.psf  > temp2.psf
+sed -e 's/   3    3      /   P    P      /g' < temp2.psf  > system.psf
+
+(If you do this, it might effect step 2 above.)

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf

@@ -0,0 +1,86 @@
+PSF
+
+       1 !NTITLE
+ REMARKS VMD generated structure x-plor psf file
+
+      28 !NATOM
+       1      1         2    2      0.000000        1.0000           0
+       2      1         1    1      0.000000        1.0000           0
+       3      1         2    2      0.000000        1.0000           0
+       4      1         1    1      0.000000        1.0000           0
+       5      1         2    2      0.000000        1.0000           0
+       6      1         1    1      0.000000        1.0000           0
+       7      1         3    3      0.000000        1.0000           0
+       8      1         3    3      0.000000        1.0000           0
+       9      1         1    1      0.000000        1.0000           0
+      10      1         2    2      0.000000        1.0000           0
+      11      1         1    1      0.000000        1.0000           0
+      12      1         2    2      0.000000        1.0000           0
+      13      1         1    1      0.000000        1.0000           0
+      14      1         2    2      0.000000        1.0000           0
+      15      1         3    3      0.000000        1.0000           0
+      16      1         3    3      0.000000        1.0000           0
+      17      1         3    3      0.000000        1.0000           0
+      18      1         1    1      0.000000        1.0000           0
+      19      1         1    1      0.000000        1.0000           0
+      20      1         2    2      0.000000        1.0000           0
+      21      1         2    2      0.000000        1.0000           0
+      22      1         1    1      0.000000        1.0000           0
+      23      1         1    1      0.000000        1.0000           0
+      24      1         2    2      0.000000        1.0000           0
+      25      1         2    2      0.000000        1.0000           0
+      26      1         1    1      0.000000        1.0000           0
+      27      1         2    2      0.000000        1.0000           0
+      28      2         4    4      0.000000      100.0000           0
+
+      26 !NBOND: bonds
+       1       2       2       3       3       4       4       5
+       5       6       6       7       7       8       8       9
+       9      10      10      11      11      12      12      13
+      13      14      14      15      15      16      16      17
+      17      18      18      19      19      20      20      21
+      21      22      22      23      23      24      24      25
+      25      26      26      27
+
+      25 !NTHETA: angles
+      13      14      15       7       8       9       6       7       8
+      16      17      18      15      16      17       2       3       4
+       4       5       6       9      10      11      11      12      13
+      14      15      16       1       2       3       3       4       5
+      10      11      12      12      13      14      25      26      27
+       5       6       7       8       9      10      17      18      19
+      18      19      20      22      23      24      21      22      23
+      19      20      21      20      21      22      23      24      25
+      24      25      26
+
+      19 !NPHI: dihedrals
+       1       2       3       4       2       3       4       5
+       3       4       5       6       4       5       6       7
+       8       9      10      11       9      10      11      12
+      10      11      12      13      11      12      13      14
+      12      13      14      15      15      16      17      18
+      16      17      18      19      17      18      19      20
+      18      19      20      21      19      20      21      22
+      20      21      22      23      21      22      23      24
+      22      23      24      25      23      24      25      26
+      24      25      26      27
+
+       0 !NIMPHI: impropers
+
+
+       0 !NDON: donors
+
+
+       0 !NACC: acceptors
+
+
+       0 !NNB
+
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0
+
+       1       0 !NGRP
+       0       0       0
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt

@@ -0,0 +1,216 @@
+# This file defines the "frustrated" coarse-grained protein model used in:
+# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
+# (http://www.pnas.org/content/101/36/13192)
+
+
+1beadFrustrated {
+
+  # There are 3 atom types (referred to above as B, L, and N)
+  # Define their masses:
+
+  write_once("Data Masses") {
+    @atom:B   1.0
+    @atom:L   1.0
+    @atom:N   1.0
+  }
+
+  #  AtomID  MoleculeID  AtomType  Charge  X        Y         Z
+
+  write('Data Atoms') {
+    $atom:a1  $mol  @atom:L  0.0   -0.92636654 -1.8409904 -2.1482679
+    $atom:a2  $mol  @atom:B  0.0   -0.57313354 -1.0670787 -1.6182341
+    $atom:a3  $mol  @atom:L  0.0   -0.85707399 -1.2358703 -0.69350966
+    $atom:a4  $mol  @atom:B  0.0   -0.44231274 -0.4584993 -0.23418709
+    $atom:a5  $mol  @atom:L  0.0   -0.75081182 -0.62868078 0.69786737
+    $atom:a6  $mol  @atom:B  0.0   -0.36201977 0.11619615 1.2249098
+    $atom:a7  $mol  @atom:N  0.0   -0.63708237 -0.15973084 2.1723919
+    $atom:a8  $mol  @atom:N  0.0   0.20516047 0.10417157 2.624901
+    $atom:a9  $mol  @atom:B  0.0   0.57223743 0.44728103 1.7695617
+    $atom:a10 $mol  @atom:L  0.0   0.77646279 -0.40630393 1.3168043
+    $atom:a11 $mol  @atom:B  0.0   0.45475664 -0.2077937 0.40045721
+    $atom:a12 $mol  @atom:L  0.0   0.72712495 -1.0397637 -0.087614951
+    $atom:a13 $mol  @atom:B  0.0   0.36971183 -0.85840501 -0.9933019
+    $atom:a14 $mol  @atom:L  0.0   0.74784336 -1.5700415 -1.5859217
+    $atom:a15 $mol  @atom:N  0.0   0.43423905 -1.2758917 -2.4853429
+    $atom:a16 $mol  @atom:N  0.0   0.70583191 -0.30726921 -2.4987711
+    $atom:a17 $mol  @atom:N  0.0   -0.091688915 0.23323014 -2.2051358
+    $atom:a18 $mol  @atom:B  0.0   -0.34243283 -0.035822049 -1.2644719
+    $atom:a19 $mol  @atom:B  0.0   0.41961247 0.18475451 -0.65971014
+    $atom:a20 $mol  @atom:L  0.0   0.51968465 1.1546791 -0.77877053
+    $atom:a21 $mol  @atom:L  0.0   -0.40827985 1.2765273 -0.52550748
+    $atom:a22 $mol  @atom:B  0.0   -0.368141 0.58090904 0.19152224
+    $atom:a23 $mol  @atom:B  0.0   0.40327249 0.86101769 0.7336255
+    $atom:a24 $mol  @atom:L  0.0   0.22707289 1.8326235 0.89673346
+    $atom:a25 $mol  @atom:L  0.0   -0.66500182 1.7285809 1.2783166
+    $atom:a26 $mol  @atom:B  0.0   -0.39205603 1.0475436 1.9328097
+    $atom:a27 $mol  @atom:L  0.0   0.25339027 1.5246265 2.5388463
+  }
+
+  # bond-ID   bond-Type      atom-ID  atom-ID
+
+  write('Data Bonds') {
+    $bond:b1 @bond:backbone  $atom:a1 $atom:a2
+    $bond:b2 @bond:backbone  $atom:a2 $atom:a3
+    $bond:b3 @bond:backbone  $atom:a3 $atom:a4
+    $bond:b4 @bond:backbone  $atom:a4 $atom:a5
+    $bond:b5 @bond:backbone  $atom:a5 $atom:a6
+    $bond:b6 @bond:backbone  $atom:a6 $atom:a7
+    $bond:b7 @bond:backbone  $atom:a7 $atom:a8
+    $bond:b8 @bond:backbone  $atom:a8 $atom:a9
+    $bond:b9 @bond:backbone  $atom:a9 $atom:a10
+    $bond:b10 @bond:backbone  $atom:a10 $atom:a11
+    $bond:b11 @bond:backbone  $atom:a11 $atom:a12
+    $bond:b12 @bond:backbone  $atom:a12 $atom:a13
+    $bond:b13 @bond:backbone  $atom:a13 $atom:a14
+    $bond:b14 @bond:backbone  $atom:a14 $atom:a15
+    $bond:b15 @bond:backbone  $atom:a15 $atom:a16
+    $bond:b16 @bond:backbone  $atom:a16 $atom:a17
+    $bond:b17 @bond:backbone  $atom:a17 $atom:a18
+    $bond:b18 @bond:backbone  $atom:a18 $atom:a19
+    $bond:b19 @bond:backbone  $atom:a19 $atom:a20
+    $bond:b20 @bond:backbone  $atom:a20 $atom:a21
+    $bond:b21 @bond:backbone  $atom:a21 $atom:a22
+    $bond:b22 @bond:backbone  $atom:a22 $atom:a23
+    $bond:b23 @bond:backbone  $atom:a23 $atom:a24
+    $bond:b24 @bond:backbone  $atom:a24 $atom:a25
+    $bond:b25 @bond:backbone  $atom:a25 $atom:a26
+    $bond:b26 @bond:backbone  $atom:a26 $atom:a27
+  }
+
+  # (3-body) Angles are specified below
+
+  # (4-body) Dihedrals must be defined explicitly for every quartet of atoms.
+  #          (These interactions are not determined by atom type.)
+
+  # dihedral-ID   dihedral-Type    atom-ID  atom-ID  atom-ID  atom-ID
+
+  write('Data Dihedrals') {
+
+    $dihedral:d1  @dihedral:beta  $atom:a1 $atom:a2 $atom:a3 $atom:a4
+    $dihedral:d2  @dihedral:beta  $atom:a2 $atom:a3 $atom:a4 $atom:a5
+    $dihedral:d3  @dihedral:beta  $atom:a3 $atom:a4 $atom:a5 $atom:a6
+    $dihedral:d4  @dihedral:beta  $atom:a4 $atom:a5 $atom:a6 $atom:a7
+
+    #    Dihedral angle forces in the turn regions were switched off
+    #    (in this model) so just I comment them out (and \ the variable names).
+    # \$dihedral:d5  \@dihedral:turn  $atom:a5 $atom:a6 $atom:a7 $atom:a8
+    # \$dihedral:d6  \@dihedral:turn  $atom:a6 $atom:a7 $atom:a8 $atom:a9
+    # \$dihedral:d7  \@dihedral:turn  $atom:a7 $atom:a8 $atom:a9 $atom:a10
+
+    $dihedral:d8  @dihedral:beta  $atom:a8 $atom:a9 $atom:a10 $atom:a11
+    $dihedral:d9  @dihedral:beta  $atom:a9 $atom:a10 $atom:a11 $atom:a12
+    $dihedral:d10  @dihedral:beta  $atom:a10 $atom:a11 $atom:a12 $atom:a13
+    $dihedral:d11  @dihedral:beta  $atom:a11 $atom:a12 $atom:a13 $atom:a14
+    $dihedral:d12  @dihedral:beta  $atom:a12 $atom:a13 $atom:a14 $atom:a15
+
+    #    Dihedral angle forces in the turn regions were switched off
+    #    (in this model) so just I comment them out (and \ the variable names).
+    # \$dihedral:d13  \@dihedral:turn  $atom:a13 $atom:a14 $atom:a15 $atom:a16
+    # \$dihedral:d14  \@dihedral:turn  $atom:a14 $atom:a15 $atom:a16 $atom:a17
+
+    $dihedral:d15  @dihedral:alpha  $atom:a15 $atom:a16 $atom:a17 $atom:a18
+    $dihedral:d16  @dihedral:alpha  $atom:a16 $atom:a17 $atom:a18 $atom:a19
+    $dihedral:d17  @dihedral:alpha  $atom:a17 $atom:a18 $atom:a19 $atom:a20
+    $dihedral:d18  @dihedral:alpha  $atom:a18 $atom:a19 $atom:a20 $atom:a21
+    $dihedral:d19  @dihedral:alpha  $atom:a19 $atom:a20 $atom:a21 $atom:a22
+    $dihedral:d20  @dihedral:alpha  $atom:a20 $atom:a21 $atom:a22 $atom:a23
+    $dihedral:d21  @dihedral:alpha  $atom:a21 $atom:a22 $atom:a23 $atom:a24
+    $dihedral:d22  @dihedral:alpha  $atom:a22 $atom:a23 $atom:a24 $atom:a25
+    $dihedral:d23  @dihedral:alpha  $atom:a23 $atom:a24 $atom:a25 $atom:a26
+    $dihedral:d24  @dihedral:alpha  $atom:a24 $atom:a25 $atom:a26 $atom:a27
+  }
+
+  # All consecutively bonded triplets of atoms same 3-body bond-angle 
+  # interaction parameters.  Of coarse, we could specify them all explicitly
+  # (as we did for the dihedrals above), but I wanted to show how to specify
+  # angles by atom type instead.  (You can do this for dihedrals & impropers
+  # also.)
+
+  #     angle-Type     atom-Type  atom-Type  atom-Type   bond-Type bond-Type
+
+  write_once('Data Angles By Type') {
+    @angle:backbone @atom:* @atom:* @atom:*  @bond:* @bond:*
+  }
+
+  # (The "*" is a wildcard character.  I use "*" to denote any atom-type or
+  #  bond-type which is defined within the current namespace: 1beadFrustrated)
+
+
+  # 2-body (non-bonded) interactions:
+  #
+  #   Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
+  #
+  #              i       j           pairstylename             eps      sig K L
+  #
+  write_once("In Settings") {
+    pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0          1.0 1 -1
+    pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0
+    pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0
+    pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1
+    pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25         1.0 1 0
+    pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0
+  }
+
+
+  # 2-body (bonded) interactions:
+  #
+  #   Ubond(r) = (k/2)*(r-0)^2
+  #
+  #   The corresponding command is:
+  #
+  #                  bond-Type   bondstylename     k    r0
+
+  write_once("In Settings") {
+    bond_coeff     @bond:backbone   harmonic    100.0  1.0
+  }
+
+  # 3-body interactions in this example are listed by atomType and bondType
+  # The atomIDs involved are determined automatically.  The forumula used is:
+  #
+  # Uangle(theta) = (k/2)*(theta-theta0)^2   
+  #     (k in kcal/mol/rad^2, theta0 in degrees)
+  #
+  #                 angle-Type   anglestylename    k         theta0
+
+  write_once("In Settings") {
+    angle_coeff    @angle:backbone  harmonic   13.3333333333  105.0
+  }
+
+
+  # We use tabular dihedral potentials to implement the dihedral forces.
+  # (Actually there is a way to use Fourier series, using multiple charmm 
+  #  style dihedral interactions, but it's slower and messier.)
+
+  write_once("In Settings") {
+    #                              style           file                 keyword
+    dihedral_coeff @dihedral:alpha table  table_dihedral_frustrated.dat FRUSTRATED_ALPHA
+    dihedral_coeff @dihedral:beta  table  table_dihedral_frustrated.dat FRUSTRATED_BETA
+    # No need to specify dihedral interactions in the turn regions. (none exist)
+  }
+
+  write_once("In Settings") {
+    # Optional: define the atoms in the "proteins" group
+    group proteins type @atom:B
+    group proteins type @atom:L
+    group proteins type @atom:N
+  }
+
+  # LAMMPS has many available force field styles (and atom styles). 
+  # Here, we pick the ones which work well for this molecular model:
+
+  write_once("In Init") {
+    # --- Default options for the "1BeadFrustrated" protein model ---
+    # ---            (These can be overridden later.)             ---
+    units           lj
+    atom_style      full
+    bond_style      hybrid harmonic
+    angle_style     hybrid harmonic
+    dihedral_style  hybrid table spline 360
+    pair_style      hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0
+    pair_modify     mix arithmetic
+    special_bonds   lj 0.0 0.0 1.0   #(turn on "1-4" interactions)
+  }
+
+} # 1beadFrustrated
+
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt

@@ -0,0 +1,85 @@
+import "1beadFrustrated.lt"
+
+
+# Alternate starting conformation (same molecule):
+
+
+1beadMisfolded inherits 1beadFrustrated {
+
+  # This molecule "inherits" all of its features from "1beadFrustrated".
+  # Here we override the atomic positions with new coordinates:
+
+  #  AtomID   MoleculeID AtomType  Charge       X        Y         Z
+
+  write("Data Atoms") {
+    $atom:a1   $mol   @atom:L    0.0   -0.69801399 -0.22114168 -1.9464876
+    $atom:a2   $mol   @atom:B    0.0   -0.40921658 -0.027063664 -1.0033251
+    $atom:a3   $mol   @atom:L    0.0   0.10259348 0.80836418 -1.0737085
+    $atom:a4   $mol   @atom:B    0.0   0.25857916 1.0054984 -0.11621451
+    $atom:a5   $mol   @atom:L    0.0   0.8258629 1.8325549 -0.18529135
+    $atom:a6   $mol   @atom:B    0.0   0.91366257 2.1950317 0.74175977
+    $atom:a7   $mol   @atom:N    0.0   1.4399539 1.554238 1.2994409
+    $atom:a8   $mol   @atom:N    0.0   0.73372573 1.0161012 1.7397275
+    $atom:a9   $mol   @atom:B    0.0   0.26608782 0.65302497 0.94353938
+    $atom:a10  $mol   @atom:L    0.0   0.97442305 0.13574211 0.50586398
+    $atom:a11  $mol   @atom:B    0.0   0.35889617 -0.18247555 -0.1764186
+    $atom:a12  $mol   @atom:L    0.0   0.87151735 -0.77260824 -0.75240916
+    $atom:a13  $mol   @atom:B    0.0   0.047726486 -1.0530682 -1.1902704
+    $atom:a14  $mol   @atom:L    0.0   0.34530697 -1.7476773 -1.8393331
+    $atom:a15  $mol   @atom:N    0.0   0.65865186 -2.45948 -1.2167056
+    $atom:a16  $mol   @atom:N    0.0   -0.16534524 -2.6219442 -0.67112167
+    $atom:a17  $mol   @atom:N    0.0   -0.010590421 -2.2445242 0.24748633
+    $atom:a18  $mol   @atom:B    0.0   0.18135771 -1.2564919 0.1767523
+    $atom:a19  $mol   @atom:B    0.0   -0.57472665 -0.82852797 -0.27027791
+    $atom:a20  $mol   @atom:L    0.0   -1.3967448 -1.0516787 0.24247346
+    $atom:a21  $mol   @atom:L    0.0   -1.003428 -0.85642681 1.1107555
+    $atom:a22  $mol   @atom:B    0.0   -0.25156735 -0.3182346 0.74262946
+    $atom:a23  $mol   @atom:B    0.0   -0.61751956 0.30115562 0.070426493
+    $atom:a24  $mol   @atom:L    0.0   -1.3347934 0.83310182 0.52625934
+    $atom:a25  $mol   @atom:L    0.0   -0.83315257 1.270904 1.2564086
+    $atom:a26  $mol   @atom:B    0.0   -0.10469759 1.6988523 0.72597181
+    $atom:a27  $mol   @atom:L    0.0   -0.57854905 2.3367737 0.11206868
+  }
+
+} # 1beadMisfolded
+
+
+1beadUnfolded inherits 1beadFrustrated {
+
+  # This molecule "inherits" all of its features from "1beadFrustrated"
+  # Here we override the atomic positions with new coordinates:
+
+  #  AtomID MoleculeID AtomType Charge   X        Y         Z
+
+  write('Data Atoms') {
+    $atom:a1   $mol   @atom:L    0.0    -2.4      1.7      -0.0
+    $atom:a2   $mol   @atom:B    0.0    -1.8      1.7       0.8
+    $atom:a3   $mol   @atom:L    0.0    -1.2      2.5       0.8
+    $atom:a4   $mol   @atom:B    0.0    -0.6      2.5      -0.0
+    $atom:a5   $mol   @atom:L    0.0     0.0      1.7      -0.0
+    $atom:a6   $mol   @atom:B    0.0     0.6      1.7       0.8
+    $atom:a7   $mol   @atom:N    0.0     1.2      2.5       0.8
+    $atom:a8   $mol   @atom:N    0.0     1.8      2.5      -0.0
+    $atom:a9   $mol   @atom:B    0.0     2.4      1.7      -0.0
+    $atom:a10  $mol   @atom:L    0.0     3.0      1.7      -0.8
+    $atom:a11  $mol   @atom:B    0.0     3.0      0.7      -0.8
+    $atom:a12  $mol   @atom:L    0.0     3.0      0.1      -0.0
+    $atom:a13  $mol   @atom:B    0.0     3.8     -0.5      -0.0
+    $atom:a14  $mol   @atom:L    0.0     3.8     -1.1      -0.8
+    $atom:a15  $mol   @atom:N    0.0     3.0     -1.7      -0.8
+    $atom:a16  $mol   @atom:N    0.0     3.0     -1.7       0.2
+    $atom:a17  $mol   @atom:N    0.0     2.4     -2.5       0.2
+    $atom:a18  $mol   @atom:B    0.0     1.8     -2.5      -0.6
+    $atom:a19  $mol   @atom:B    0.0     1.2     -1.7      -0.6
+    $atom:a20  $mol   @atom:L    0.0     0.6     -1.7       0.2
+    $atom:a21  $mol   @atom:L    0.0    -0.0     -2.5       0.2
+    $atom:a22  $mol   @atom:B    0.0    -0.6     -2.5      -0.6
+    $atom:a23  $mol   @atom:B    0.0    -1.2     -1.7      -0.6
+    $atom:a24  $mol   @atom:L    0.0    -1.8     -1.7       0.2
+    $atom:a25  $mol   @atom:L    0.0    -2.4     -2.5       0.2
+    $atom:a26  $mol   @atom:B    0.0    -3.0     -2.5      -0.6
+    $atom:a27  $mol   @atom:L    0.0    -3.6     -1.7      -0.6
+  }
+
+} # 1beadUnfolded
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt

@@ -0,0 +1,41 @@
+# Here we define a trivial molecule containing only one particle.
+
+Chaperonin {
+
+  # atomID molID atomType charge   x  y  z
+
+  write("Data Atoms") {
+    $atom:C $mol @atom:C   0.0   0.0 0.0 0.0
+  }
+
+  write_once("Data Masses") {
+    @atom:C 100.0
+  }
+
+  write_once("In Settings") {
+    # If for some reason there are multiple chaperones present, 
+    # I assume that they interact repulsively (hence, L=0)
+    #            i       j                              epsilon sigma K L
+
+    pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0   6.0  1 0
+
+    # Optional: define the atoms in the "chaperonins" group:
+    # (Defining a group for the chaperone makes it easy to immobilize it later.)
+
+    group chaperonins type @atom:C
+  }
+
+
+  # Specify which pair_styles, and atom styles work well with 
+  # this model.  (Again this can be overridden later.)
+
+  write_once("In Init") {
+    units       lj
+    atom_style  full
+    pair_style  hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 11.0 12.0
+  }
+
+} # Chaperonin
+
+# We have not specified how this particle interacts with other particles
+# besides itself.  Later on you must do this.

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py

@@ -0,0 +1,87 @@
+#!/usr/bin/env python
+
+# Calculate a table of pairwise energies and forces between atoms in the 
+# protein and a chaperone provided in the supplemental materials section of:
+# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
+# This is stored in a tabulated force field with a singularity at a distance R.
+#
+# To calculate the table for interaction between 
+# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table:
+#   ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181
+# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table:
+#   ./calc_chaperone_table.py 1.0 1.0 6.0 0.0   0.0 5.9 1181
+# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table:
+#   ./calc_chaperone_table.py 1.0 1.0 3.0 0.60  3.1 8.0 981 True
+# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table:
+#   ./calc_chaperone_table.py 1.0 1.0 3.0 0.0   3.1 8.0 981 True
+
+from math import *
+import sys
+
+def U(r, eps, sigma, R, h):
+    #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h))
+    # Formula is undefined at r=0, but you can take the limit:
+    if r <= 0:
+        return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0)
+                               - h*pow((sigma/R), 6.0))
+    xp = sigma/(r+R)
+    xm = sigma/(r-R)
+    term10 = pow(xm, 10.0) - pow(xp, 10.0)
+    term4  = pow(xm, 4.0)  - pow(xp, 4.0)
+    return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4)
+
+def F(r, eps, sigma, R, h):
+    # Formula is undefined at r=0, but you can take the limit:
+    if r <= 0:
+        return 0.0
+    product_term_a = U(r, eps, sigma, R, h) / r
+    ixp = (r+R)/sigma
+    ixm = (r-R)/sigma
+    dix_dr = 1.0/sigma
+    term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0))
+    term4  =  (4.0/sigma)*(pow(ixm, -5.0)  - pow(ixp, -5.0))
+    product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4)
+    return product_term_a + product_term_b
+    
+
+class InputError(Exception):
+    """ A generic exception object containing a string for error reporting.
+
+    """
+    def __init__(self, err_msg):
+        self.err_msg = err_msg
+    def __str__(self):
+        return self.err_msg
+    def __repr__(self):
+        return str(self)
+
+if len(sys.argv) < 8:
+    sys.stderr.write("Error: expected 7 arguments:\n"
+                     "\n"
+                     "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n")
+    sys.exit(-1)
+
+epsilon = float(sys.argv[1])
+sigma   = float(sys.argv[2])
+R       = float(sys.argv[3])
+h       = float(sys.argv[4])
+rmin    = float(sys.argv[5])
+rmax    = float(sys.argv[6])
+N       = int(sys.argv[7])
+
+subtract_Urcut = False
+if len(sys.argv) == 9:
+    subtract_Urcut = True
+rcut    = rmax
+
+for i in range(0,N):
+    r = rmin + i*(rmax-rmin)/(N-1)
+    U_r = U(r, epsilon, sigma, R, h) 
+    F_r = F(r, epsilon, sigma, R, h)
+    if subtract_Urcut:
+        U_r -= U(rcut, epsilon, sigma, R, h)
+        if (r >= rcut) or (i==N-1):
+            U_r = 0.0
+            F_r = 0.0
+    print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py

@@ -0,0 +1,67 @@
+#!/usr/bin/env python
+
+# Calculate a table of dihedral angle interactions used in the alpha-helix
+# and beta-sheet regions of the frustrated protein model described in
+#  provided in figure 8 of the supplemental materials section of:
+# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
+# Note that the "A" and "B" parameters were incorrectly reported to be 
+# 5.4*epsilon and 6.0*epsilon.  The values used were 5.6 and 6.0 epsilon.
+# The phiA and phiB values were 57.29577951308232 degrees (1 rad) 
+# and 180 degrees, respectively.  Both expA and expB were 6.0.
+#
+# To generate the table used for the alpha-helix (1 degree resolution) use this:
+#  ./calc_dihedral_table.py 6.0 57.29577951308232 6  5.6 180 6  0.0 359  360
+# To generate the table used for the beta-sheets (1 degree resolution) use this:
+#  ./calc_dihedral_table.py 5.6 57.29577951308232 6  6.0 180 6  0.0 359  360
+#
+# (If you're curious as to why I set the location of the minima at phi_alpha
+#  to 1.0 radians (57.2957795 degrees), there was no particularly good reason.
+#  I think the correct value turns out to be something closer to 50 degrees.)
+
+
+from math import *
+import sys
+
+
+# The previous version included the repulsive core term
+def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
+    conv_units = pi/180.0
+    if use_radians:
+        conv_units = 1.0
+    termA = pow(cos(0.5*(phi-phiA)*conv_units), expA)
+    termB = pow(cos(0.5*(phi-phiB)*conv_units), expB)
+    return -A*termA - B*termB
+
+# The previous version included the repulsive core term
+def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
+    conv_units = pi/180.0
+    if use_radians:
+        conv_units = 1.0
+    termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * 
+             expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0))
+    termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * 
+             expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0))
+    return -conv_units*(A*termA + B*termB)
+
+if len(sys.argv) != 10:
+    sys.stderr.write("Error: expected 9 arguments:\n"
+                     "\n"
+                     "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n")
+    sys.exit(-1)
+
+A       = float(sys.argv[1])
+phiA    = float(sys.argv[2])
+expA    = float(sys.argv[3])
+B       = float(sys.argv[4])
+phiB    = float(sys.argv[5])
+expB    = float(sys.argv[6])
+phi_min = float(sys.argv[7])
+phi_max = float(sys.argv[8])
+N       =   int(sys.argv[9])
+
+for i in range(0,N):
+    phi = phi_min + i*(phi_max - phi_min)/(N-1)
+    U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
+    F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
+    print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi))
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt

@@ -0,0 +1,45 @@
+write_once("Data Boundary") {
+  0.0  20.0  xlo xhi
+  0.0  20.0  ylo yhi
+  0.0  20.0  zlo zhi
+}
+
+
+import "1beadFrustrated_variants.lt"
+import "chaperonin.lt"
+
+
+protein    = new 1beadMisfolded # (frustrated protein, misfolded conformation)
+chaperinin = new Chaperonin     # (hollow chaperonin cavity. usually immobile)
+
+
+
+# ---- Now define interactions between the atoms in the protein ----
+# ---- (named "B", "L", "N") and the atom which represents the  ----
+# ---- chaperone ("C").  These interactions are tabulated.      ----
+
+write_once("In Settings") {
+  pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/B  table  table_chaperonin_h=0.475.dat CH_H0.475
+  pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/L  table  table_chaperonin_h=0.dat CH_H0
+  pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/N  table  table_chaperonin_h=0.dat CH_H0
+}
+
+# Note: If you want to use a "hydrophilic" chaperone (with h=0, not h=0.475)
+#       then replace "table_chaperonin_h=0_475.dat CH_H0.475"
+#       with "table_chaperonin_h=0.dat CH_H0"
+
+# LAMMPS has many available force field styles (and atom styles).  Here we
+# select the ones which work well for the full combine system.  (This should 
+# override any settings made in "1beadFrustrated.lt" or "chaperonin.lt")
+
+
+write_once("In Init") {
+  units           lj
+  atom_style      full
+  bond_style      hybrid harmonic
+  angle_style     hybrid harmonic
+  dihedral_style  hybrid table spline 360
+  pair_style      hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 1181
+  pair_modify     mix arithmetic
+  special_bonds   lj 0.0 0.0 1.0   #(turn on "1-4" interactions)
+}

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_dihedral_frustrated.dat

@@ -0,0 +1,735 @@
+# Table of the potential and its negative derivative for frustrated alpha helix
+# (Note: Derivatives are in units of energy/radians, not energy/degrees.)
+# ./calc_dihedral_table.py 6.0 57.29577951308232 6  5.6 180 6  0.0 359  360
+
+FRUSTRATED_ALPHA
+N 360 DEGREES
+
+1 0.0 -2.74081145103 0.0783990792662
+2 1.0 -2.81950869101 0.0789852583442
+3 2.0 -2.89876136749 0.0795096391909
+4 3.0 -2.97850675562 0.0799703813963
+5 4.0 -3.05868032959 0.0803657243943
+6 5.0 -3.13921584545 0.0806939935737
+7 6.0 -3.22004543014 0.0809536062381
+8 7.0 -3.30109967628 0.0811430773977
+9 8.0 -3.38230774267 0.0812610253741
+10 9.0 -3.46359746038 0.0813061772009
+11 10.0 -3.54489544401 0.0812773738039
+12 11.0 -3.62612720812 0.0811735749433
+13 12.0 -3.70721728841 0.0809938639029
+14 13.0 -3.78808936748 0.080737451911
+15 14.0 -3.86866640485 0.0804036822781
+16 15.0 -3.94887077101 0.0799920342374
+17 16.0 -4.02862438516 0.0795021264757
+18 17.0 -4.10784885622 0.0789337203415
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+
+# Table of the potential and its negative derivative for frustrated beta sheet
+# (Note: Derivatives are in units of energy/radians, not energy/degrees.)
+#  ./calc_dihedral_table.py 5.6 57.29577951308232 6  6.0 180 6  0.0 359  360
+
+FRUSTRATED_BETA
+N 360 DEGREES
+
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tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min

@@ -0,0 +1,25 @@
+# -- Init section --
+
+include system.in.init
+
+# -- Atom definition section --
+
+read_data system.data
+
+# -- Settings Section --
+
+include system.in.settings
+
+# Optional: Make sure the pairwise energies look reasonable:
+pair_write 1 4 1001 r 0.00000000001 5.05 test_chap-B.dat C-B 0 0
+pair_write 2 4 1001 r 0.00000000001 5.05 test_chap-L.dat C-L 0 0
+pair_write 3 4 1001 r 0.00000000001 5.05 test_chap-N.dat C-N 0 0
+
+
+# -- Run section --
+
+dump            1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
+
+minimize 1.0e-5 1.0e-7 500 2000
+
+write_restart  system_after_min.rst

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt

@@ -0,0 +1,48 @@
+# -- Init Section --
+
+include system.in.init
+
+# -- Atom Definition Section --
+
+# I you want to be careful, you can minimize the system first.  (Try using 
+# "run.in.min" and uncomment the read_restart command in this file below.)
+# read_restart system_after_min.rst
+
+read_data system.data
+
+# -- Settings Section --
+
+include system.in.settings
+
+# -- Run Section --
+
+
+timestep        0.025
+dump            1 all custom 50000 traj_nvt.lammpstrj id mol type x y z ix iy iz
+
+# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve".
+# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
+
+# Keep the chaperonin fixed.  Only let the protein move.
+
+fix fxlan proteins langevin 0.25 0.25 1.0 48279
+fix fxnve proteins nve
+
+# Notes:
+# The temperature is in reduced units and is set to 0.25
+# which is the folding temperature for the frustrated protein
+# The inverse-damping-rate "damp" (which has units of time) is set to 1.0,
+# as it was in the paper.  (Hopefully folding times should be similar.)
+# (See http://lammps.sandia.gov/doc/fix_langevin.html)
+
+
+thermo_style    custom step temp pe etotal press vol epair ebond eangle edihed
+thermo_modify   norm no  #(report total energy not energy / num_atoms)
+thermo          50000     #(time interval for printing out "thermo" data)
+
+#restart         100000000  restart_nvt
+
+run		1000000000
+
+write_restart  system_after_nvt.rst
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT

@@ -0,0 +1,38 @@
+# This directory demonstrates how to run a long simulation of 
+# the "frustrated" coarse-grained protein in the presence of one
+# or more coarse-graine small ("mini") chaperones (R=3, h=0.6) as described in:
+#
+# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006)
+#   and earlier in:
+# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
+#
+# Because this process takes a long time (even with the help of the chaperone)
+# I save the data relatively infrequently.
+#
+# Note: In the 2006 paper, only one protein and one chaperone was simulated.
+#       In this example, 8 proteins and 8 chaperones were simulated.
+#
+# Note: In this case, the chaperones appear to catalyze aggregation.
+#       This is due to an artifact in the protein model.  That model 
+#       was not designed to study aggregation.  However the simulation
+#       is suitable for making pretty pictures (to show off moltemplate).
+#
+# -------- REQUIREMENTS: ---------
+# 1) This example requires the "USER-MISC" package.  (Use "make yes-USER-MISC")
+#   http://lammps.sandia.gov/doc/Section_start.html#start_3
+# 2) It also may require additional features and bug fixes for LAMMPS.
+#   be sure to download and copy the "additional_lammps_code" from 
+#   http://moltemplate.org     (upper-left corner menu)
+# 3) Unpack it
+# 4) copy the .cpp and .h files to the src folding of your lammps installation.
+# 5) Compile LAMMPS.
+
+-------------
+Instructions on how to build LAMMPS input files and 
+run a short simulation are provided in other README files.
+
+step 1)
+README_setup.sh
+
+step2)
+README_run.sh

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh

@@ -0,0 +1,31 @@
+# You would probably run lammps this way:
+#
+# lmp_ubuntu -i run.in.nvt
+
+# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer
+# to the input scripts & data files you created earlier when you ran moltemplate
+# system.in.init, system.in.settings, system.data
+
+
+
+
+# -----------------------------------
+
+
+
+LAMMPS_COMMAND="lmp_ubuntu"
+
+# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
+# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary.
+
+# Run lammps using the following 3 commands:
+
+"$LAMMPS_COMMAND" -i run.in.min    # minimize         (OPTIONAL)
+"$LAMMPS_COMMAND" -i run.in.nvt    # production run
+
+# Alternately, if you have MPI installed, try something like this:
+
+#NUMPROCS=4
+#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min    # minimize  (OPTIONAL)
+#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt    # production run
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh

@@ -0,0 +1,24 @@
+# Use these commands to generate the LAMMPS input script and data file
+# (and other auxilliary files):
+
+
+# Create LAMMPS input files this way:
+cd moltemplate_files
+
+  # run moltemplate
+
+  moltemplate.sh -overlay-dihdedrals system.lt
+
+  # This will generate various files with names ending in *.in* and *.data. 
+  # These files are the input files directly read by LAMMPS.  Move them to 
+  # the parent directory (or wherever you plan to run the simulation).
+
+  mv -f system.in* system.data ../
+  cp -r table*.dat ../
+
+  # Optional:
+  # The "./output_ttree/" directory is full of temporary files generated by 
+  # moltemplate.  They can be useful for debugging, but are usually thrown away.
+  rm -rf output_ttree/
+
+cd ../

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt

@@ -0,0 +1,87 @@
+
+ ------- To view a lammps trajectory in VMD --------
+
+
+1) Build a PSF file for use in viewing with VMD.
+
+This step works with VMD 1.9 and topotools 1.2.  
+(Older versions, like VMD 1.8.6, don't support this.)
+
+
+a) Start VMD
+b) Menu  Extensions->Tk Console
+c) Enter:
+
+(I assume that the the DATA file is called "system.data")
+
+   topo readlammpsdata system.data full
+   animate write psf system.psf
+
+2) 
+
+Later, to Load a trajectory in VMD:
+
+  Start VMD
+  Select menu: File->New Molecule
+ -Browse to select the PSF file you created above, and load it.
+  (Don't close the window yet.)
+ -Browse to select the trajectory file.
+  If necessary, for "file type" select: "LAMMPS Trajectory"
+  Load it.
+
+   ----  A note on trajectory format: -----
+If the trajectory is a DUMP file, then make sure the it contains the
+information you need for pbctools (see below.  I've been using this 
+command in my LAMMPS scripts to create the trajectories:
+
+  dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
+
+It's a good idea to use an atom_style which supports molecule-ID numbers 
+so that you can assign a molecule-ID number to each atom.  (I think this 
+is needed to wrap atom coordinates without breaking molecules in half.)
+
+Of course, you don't have to save your trajectories in DUMP format, 
+(other formats like DCD work fine)  I just mention dump files 
+because these are the files I'm familiar with.
+
+3) -----  Wrap the coordinates to the unit cell
+          (without cutting the molecules in half)
+
+a) Start VMD
+b) Load the trajectory in VMD (see above)
+c) Menu  Extensions->Tk Console
+d) Try entering these commands:
+
+    pbc wrap -compound res -all
+    pbc box
+
+    ----- Optional ----
+    Sometimes the solvent or membrane obscures the view of the solute.
+    It can help to shift the location of the periodic boundary box 
+    To shift the box in the y direction (for example) do this:
+
+    pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
+    pbc box -shiftcenterrel {0.0 0.15 0.0}
+
+    Distances are measured in units of box-length fractions, not Angstroms.
+
+    Alternately if you have a solute whose atoms are all of type 1, 
+    then you can also try this to center the box around it:
+
+    pbc wrap -sel type=1 -all -centersel type=2 -center com
+
+4) 
+    You should check if your periodic boundary conditions are too small.
+    To do that:
+       select Graphics->Representations menu option
+       click on the "Periodic" tab, and 
+       click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
+
+5) Optional: If you like, change the atom types in the PSF file so 
+   that VMD recognizes the atom types, use something like:
+
+sed -e 's/   1    1      /   C    C      /g' < system.psf > temp1.psf
+sed -e 's/   2    2      /   H    H      /g' < temp1.psf  > temp2.psf
+sed -e 's/   3    3      /   P    P      /g' < temp2.psf  > system.psf
+
+(If you do this, it might effect step 2 above.)

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf

@@ -0,0 +1,476 @@
+PSF
+
+       1 !NTITLE
+ REMARKS VMD generated structure x-plor psf file
+
+     224 !NATOM
+       1      1         2    2      0.000000        1.0000           0
+       2      1         1    1      0.000000        1.0000           0
+       3      1         2    2      0.000000        1.0000           0
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+     140      6         2    2      0.000000        1.0000           0
+     141      6         1    1      0.000000        1.0000           0
+     142      6         3    3      0.000000        1.0000           0
+     143      6         3    3      0.000000        1.0000           0
+     144      6         1    1      0.000000        1.0000           0
+     145      6         2    2      0.000000        1.0000           0
+     146      6         1    1      0.000000        1.0000           0
+     147      6         2    2      0.000000        1.0000           0
+     148      6         1    1      0.000000        1.0000           0
+     149      6         2    2      0.000000        1.0000           0
+     150      6         3    3      0.000000        1.0000           0
+     151      6         3    3      0.000000        1.0000           0
+     152      6         3    3      0.000000        1.0000           0
+     153      6         1    1      0.000000        1.0000           0
+     154      6         1    1      0.000000        1.0000           0
+     155      6         2    2      0.000000        1.0000           0
+     156      6         2    2      0.000000        1.0000           0
+     157      6         1    1      0.000000        1.0000           0
+     158      6         1    1      0.000000        1.0000           0
+     159      6         2    2      0.000000        1.0000           0
+     160      6         2    2      0.000000        1.0000           0
+     161      6         1    1      0.000000        1.0000           0
+     162      6         2    2      0.000000        1.0000           0
+     163      7         2    2      0.000000        1.0000           0
+     164      7         1    1      0.000000        1.0000           0
+     165      7         2    2      0.000000        1.0000           0
+     166      7         1    1      0.000000        1.0000           0
+     167      7         2    2      0.000000        1.0000           0
+     168      7         1    1      0.000000        1.0000           0
+     169      7         3    3      0.000000        1.0000           0
+     170      7         3    3      0.000000        1.0000           0
+     171      7         1    1      0.000000        1.0000           0
+     172      7         2    2      0.000000        1.0000           0
+     173      7         1    1      0.000000        1.0000           0
+     174      7         2    2      0.000000        1.0000           0
+     175      7         1    1      0.000000        1.0000           0
+     176      7         2    2      0.000000        1.0000           0
+     177      7         3    3      0.000000        1.0000           0
+     178      7         3    3      0.000000        1.0000           0
+     179      7         3    3      0.000000        1.0000           0
+     180      7         1    1      0.000000        1.0000           0
+     181      7         1    1      0.000000        1.0000           0
+     182      7         2    2      0.000000        1.0000           0
+     183      7         2    2      0.000000        1.0000           0
+     184      7         1    1      0.000000        1.0000           0
+     185      7         1    1      0.000000        1.0000           0
+     186      7         2    2      0.000000        1.0000           0
+     187      7         2    2      0.000000        1.0000           0
+     188      7         1    1      0.000000        1.0000           0
+     189      7         2    2      0.000000        1.0000           0
+     190      8         2    2      0.000000        1.0000           0
+     191      8         1    1      0.000000        1.0000           0
+     192      8         2    2      0.000000        1.0000           0
+     193      8         1    1      0.000000        1.0000           0
+     194      8         2    2      0.000000        1.0000           0
+     195      8         1    1      0.000000        1.0000           0
+     196      8         3    3      0.000000        1.0000           0
+     197      8         3    3      0.000000        1.0000           0
+     198      8         1    1      0.000000        1.0000           0
+     199      8         2    2      0.000000        1.0000           0
+     200      8         1    1      0.000000        1.0000           0
+     201      8         2    2      0.000000        1.0000           0
+     202      8         1    1      0.000000        1.0000           0
+     203      8         2    2      0.000000        1.0000           0
+     204      8         3    3      0.000000        1.0000           0
+     205      8         3    3      0.000000        1.0000           0
+     206      8         3    3      0.000000        1.0000           0
+     207      8         1    1      0.000000        1.0000           0
+     208      8         1    1      0.000000        1.0000           0
+     209      8         2    2      0.000000        1.0000           0
+     210      8         2    2      0.000000        1.0000           0
+     211      8         1    1      0.000000        1.0000           0
+     212      8         1    1      0.000000        1.0000           0
+     213      8         2    2      0.000000        1.0000           0
+     214      8         2    2      0.000000        1.0000           0
+     215      8         1    1      0.000000        1.0000           0
+     216      8         2    2      0.000000        1.0000           0
+     217      9         4    4      0.000000      100.0000           0
+     218      10        4    4      0.000000      100.0000           0
+     219      11        4    4      0.000000      100.0000           0
+     220      12        4    4      0.000000      100.0000           0
+     221      13        4    4      0.000000      100.0000           0
+     222      14        4    4      0.000000      100.0000           0
+     223      15        4    4      0.000000      100.0000           0
+     224      16        4    4      0.000000      100.0000           0
+
+     208 !NBOND: bonds
+       1       2       2       3       3       4       4       5
+       5       6       6       7       7       8       8       9
+       9      10      10      11      11      12      12      13
+      13      14      14      15      15      16      16      17
+      17      18      18      19      19      20      20      21
+      21      22      22      23      23      24      24      25
+      25      26      26      27      28      29      29      30
+      30      31      31      32      32      33      33      34
+      34      35      35      36      36      37      37      38
+      38      39      39      40      40      41      41      42
+      42      43      43      44      44      45      45      46
+      46      47      47      48      48      49      49      50
+      50      51      51      52      52      53      53      54
+      55      56      56      57      57      58      58      59
+      59      60      60      61      61      62      62      63
+      63      64      64      65      65      66      66      67
+      67      68      68      69      69      70      70      71
+      71      72      72      73      73      74      74      75
+      75      76      76      77      77      78      78      79
+      79      80      80      81      82      83      83      84
+      84      85      85      86      86      87      87      88
+      88      89      89      90      90      91      91      92
+      92      93      93      94      94      95      95      96
+      96      97      97      98      98      99      99     100
+     100     101     101     102     102     103     103     104
+     104     105     105     106     106     107     107     108
+     109     110     110     111     111     112     112     113
+     113     114     114     115     115     116     116     117
+     117     118     118     119     119     120     120     121
+     121     122     122     123     123     124     124     125
+     125     126     126     127     127     128     128     129
+     129     130     130     131     131     132     132     133
+     133     134     134     135     136     137     137     138
+     138     139     139     140     140     141     141     142
+     142     143     143     144     144     145     145     146
+     146     147     147     148     148     149     149     150
+     150     151     151     152     152     153     153     154
+     154     155     155     156     156     157     157     158
+     158     159     159     160     160     161     161     162
+     163     164     164     165     165     166     166     167
+     167     168     168     169     169     170     170     171
+     171     172     172     173     173     174     174     175
+     175     176     176     177     177     178     178     179
+     179     180     180     181     181     182     182     183
+     183     184     184     185     185     186     186     187
+     187     188     188     189     190     191     191     192
+     192     193     193     194     194     195     195     196
+     196     197     197     198     198     199     199     200
+     200     201     201     202     202     203     203     204
+     204     205     205     206     206     207     207     208
+     208     209     209     210     210     211     211     212
+     212     213     213     214     214     215     215     216
+
+     200 !NTHETA: angles
+      13      14      15      40      41      42      67      68      69
+      94      95      96     121     122     123     148     149     150
+     175     176     177     202     203     204       7       8       9
+       6       7       8      16      17      18      34      35      36
+      33      34      35      43      44      45      61      62      63
+      60      61      62      70      71      72      88      89      90
+      87      88      89      97      98      99     115     116     117
+     114     115     116     124     125     126     142     143     144
+     141     142     143     151     152     153     169     170     171
+     168     169     170     178     179     180     196     197     198
+     195     196     197     205     206     207      15      16      17
+      42      43      44      69      70      71      96      97      98
+     123     124     125     150     151     152     177     178     179
+     204     205     206       2       3       4       4       5       6
+       9      10      11      11      12      13      29      30      31
+      31      32      33      36      37      38      38      39      40
+      56      57      58      58      59      60      63      64      65
+      65      66      67      83      84      85      85      86      87
+      90      91      92      92      93      94     110     111     112
+     112     113     114     117     118     119     119     120     121
+     137     138     139     139     140     141     144     145     146
+     146     147     148     164     165     166     166     167     168
+     171     172     173     173     174     175     191     192     193
+     193     194     195     198     199     200     200     201     202
+      14      15      16      41      42      43      68      69      70
+      95      96      97     122     123     124     149     150     151
+     176     177     178     203     204     205       1       2       3
+       3       4       5      10      11      12      12      13      14
+      25      26      27      28      29      30      30      31      32
+      37      38      39      39      40      41      52      53      54
+      55      56      57      57      58      59      64      65      66
+      66      67      68      79      80      81      82      83      84
+      84      85      86      91      92      93      93      94      95
+     106     107     108     109     110     111     111     112     113
+     118     119     120     120     121     122     133     134     135
+     136     137     138     138     139     140     145     146     147
+     147     148     149     160     161     162     163     164     165
+     165     166     167     172     173     174     174     175     176
+     187     188     189     190     191     192     192     193     194
+     199     200     201     201     202     203     214     215     216
+       5       6       7       8       9      10      32      33      34
+      35      36      37      59      60      61      62      63      64
+      86      87      88      89      90      91     113     114     115
+     116     117     118     140     141     142     143     144     145
+     167     168     169     170     171     172     194     195     196
+     197     198     199      17      18      19      44      45      46
+      71      72      73      98      99     100     125     126     127
+     152     153     154     179     180     181     206     207     208
+      18      19      20      22      23      24      21      22      23
+      45      46      47      49      50      51      48      49      50
+      72      73      74      76      77      78      75      76      77
+      99     100     101     103     104     105     102     103     104
+     126     127     128     130     131     132     129     130     131
+     153     154     155     157     158     159     156     157     158
+     180     181     182     184     185     186     183     184     185
+     207     208     209     211     212     213     210     211     212
+      19      20      21      20      21      22      23      24      25
+      24      25      26      46      47      48      47      48      49
+      50      51      52      51      52      53      73      74      75
+      74      75      76      77      78      79      78      79      80
+     100     101     102     101     102     103     104     105     106
+     105     106     107     127     128     129     128     129     130
+     131     132     133     132     133     134     154     155     156
+     155     156     157     158     159     160     159     160     161
+     181     182     183     182     183     184     185     186     187
+     186     187     188     208     209     210     209     210     211
+     212     213     214     213     214     215
+
+     152 !NPHI: dihedrals
+       1       2       3       4       2       3       4       5
+       3       4       5       6       4       5       6       7
+       8       9      10      11       9      10      11      12
+      10      11      12      13      11      12      13      14
+      12      13      14      15      15      16      17      18
+      16      17      18      19      17      18      19      20
+      18      19      20      21      19      20      21      22
+      20      21      22      23      21      22      23      24
+      22      23      24      25      23      24      25      26
+      24      25      26      27      28      29      30      31
+      29      30      31      32      30      31      32      33
+      31      32      33      34      35      36      37      38
+      36      37      38      39      37      38      39      40
+      38      39      40      41      39      40      41      42
+      42      43      44      45      43      44      45      46
+      44      45      46      47      45      46      47      48
+      46      47      48      49      47      48      49      50
+      48      49      50      51      49      50      51      52
+      50      51      52      53      51      52      53      54
+      55      56      57      58      56      57      58      59
+      57      58      59      60      58      59      60      61
+      62      63      64      65      63      64      65      66
+      64      65      66      67      65      66      67      68
+      66      67      68      69      69      70      71      72
+      70      71      72      73      71      72      73      74
+      72      73      74      75      73      74      75      76
+      74      75      76      77      75      76      77      78
+      76      77      78      79      77      78      79      80
+      78      79      80      81      82      83      84      85
+      83      84      85      86      84      85      86      87
+      85      86      87      88      89      90      91      92
+      90      91      92      93      91      92      93      94
+      92      93      94      95      93      94      95      96
+      96      97      98      99      97      98      99     100
+      98      99     100     101      99     100     101     102
+     100     101     102     103     101     102     103     104
+     102     103     104     105     103     104     105     106
+     104     105     106     107     105     106     107     108
+     109     110     111     112     110     111     112     113
+     111     112     113     114     112     113     114     115
+     116     117     118     119     117     118     119     120
+     118     119     120     121     119     120     121     122
+     120     121     122     123     123     124     125     126
+     124     125     126     127     125     126     127     128
+     126     127     128     129     127     128     129     130
+     128     129     130     131     129     130     131     132
+     130     131     132     133     131     132     133     134
+     132     133     134     135     136     137     138     139
+     137     138     139     140     138     139     140     141
+     139     140     141     142     143     144     145     146
+     144     145     146     147     145     146     147     148
+     146     147     148     149     147     148     149     150
+     150     151     152     153     151     152     153     154
+     152     153     154     155     153     154     155     156
+     154     155     156     157     155     156     157     158
+     156     157     158     159     157     158     159     160
+     158     159     160     161     159     160     161     162
+     163     164     165     166     164     165     166     167
+     165     166     167     168     166     167     168     169
+     170     171     172     173     171     172     173     174
+     172     173     174     175     173     174     175     176
+     174     175     176     177     177     178     179     180
+     178     179     180     181     179     180     181     182
+     180     181     182     183     181     182     183     184
+     182     183     184     185     183     184     185     186
+     184     185     186     187     185     186     187     188
+     186     187     188     189     190     191     192     193
+     191     192     193     194     192     193     194     195
+     193     194     195     196     197     198     199     200
+     198     199     200     201     199     200     201     202
+     200     201     202     203     201     202     203     204
+     204     205     206     207     205     206     207     208
+     206     207     208     209     207     208     209     210
+     208     209     210     211     209     210     211     212
+     210     211     212     213     211     212     213     214
+     212     213     214     215     213     214     215     216
+
+       0 !NIMPHI: impropers
+
+
+       0 !NDON: donors
+
+
+       0 !NACC: acceptors
+
+
+       0 !NNB
+
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+
+
+       1       0 !NGRP
+       0       0       0
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt

@@ -0,0 +1,216 @@
+# This file defines the "frustrated" coarse-grained protein model used in:
+# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
+# (http://www.pnas.org/content/101/36/13192)
+
+
+1beadFrustrated {
+
+  # There are 3 atom types (referred to above as B, L, and N)
+  # Define their masses:
+
+  write_once("Data Masses") {
+    @atom:B   1.0
+    @atom:L   1.0
+    @atom:N   1.0
+  }
+
+  #  AtomID  MoleculeID  AtomType  Charge  X        Y         Z
+
+  write('Data Atoms') {
+    $atom:a1  $mol  @atom:L  0.0   -0.92636654 -1.8409904 -2.1482679
+    $atom:a2  $mol  @atom:B  0.0   -0.57313354 -1.0670787 -1.6182341
+    $atom:a3  $mol  @atom:L  0.0   -0.85707399 -1.2358703 -0.69350966
+    $atom:a4  $mol  @atom:B  0.0   -0.44231274 -0.4584993 -0.23418709
+    $atom:a5  $mol  @atom:L  0.0   -0.75081182 -0.62868078 0.69786737
+    $atom:a6  $mol  @atom:B  0.0   -0.36201977 0.11619615 1.2249098
+    $atom:a7  $mol  @atom:N  0.0   -0.63708237 -0.15973084 2.1723919
+    $atom:a8  $mol  @atom:N  0.0   0.20516047 0.10417157 2.624901
+    $atom:a9  $mol  @atom:B  0.0   0.57223743 0.44728103 1.7695617
+    $atom:a10 $mol  @atom:L  0.0   0.77646279 -0.40630393 1.3168043
+    $atom:a11 $mol  @atom:B  0.0   0.45475664 -0.2077937 0.40045721
+    $atom:a12 $mol  @atom:L  0.0   0.72712495 -1.0397637 -0.087614951
+    $atom:a13 $mol  @atom:B  0.0   0.36971183 -0.85840501 -0.9933019
+    $atom:a14 $mol  @atom:L  0.0   0.74784336 -1.5700415 -1.5859217
+    $atom:a15 $mol  @atom:N  0.0   0.43423905 -1.2758917 -2.4853429
+    $atom:a16 $mol  @atom:N  0.0   0.70583191 -0.30726921 -2.4987711
+    $atom:a17 $mol  @atom:N  0.0   -0.091688915 0.23323014 -2.2051358
+    $atom:a18 $mol  @atom:B  0.0   -0.34243283 -0.035822049 -1.2644719
+    $atom:a19 $mol  @atom:B  0.0   0.41961247 0.18475451 -0.65971014
+    $atom:a20 $mol  @atom:L  0.0   0.51968465 1.1546791 -0.77877053
+    $atom:a21 $mol  @atom:L  0.0   -0.40827985 1.2765273 -0.52550748
+    $atom:a22 $mol  @atom:B  0.0   -0.368141 0.58090904 0.19152224
+    $atom:a23 $mol  @atom:B  0.0   0.40327249 0.86101769 0.7336255
+    $atom:a24 $mol  @atom:L  0.0   0.22707289 1.8326235 0.89673346
+    $atom:a25 $mol  @atom:L  0.0   -0.66500182 1.7285809 1.2783166
+    $atom:a26 $mol  @atom:B  0.0   -0.39205603 1.0475436 1.9328097
+    $atom:a27 $mol  @atom:L  0.0   0.25339027 1.5246265 2.5388463
+  }
+
+  # bond-ID   bond-Type      atom-ID  atom-ID
+
+  write('Data Bonds') {
+    $bond:b1 @bond:backbone  $atom:a1 $atom:a2
+    $bond:b2 @bond:backbone  $atom:a2 $atom:a3
+    $bond:b3 @bond:backbone  $atom:a3 $atom:a4
+    $bond:b4 @bond:backbone  $atom:a4 $atom:a5
+    $bond:b5 @bond:backbone  $atom:a5 $atom:a6
+    $bond:b6 @bond:backbone  $atom:a6 $atom:a7
+    $bond:b7 @bond:backbone  $atom:a7 $atom:a8
+    $bond:b8 @bond:backbone  $atom:a8 $atom:a9
+    $bond:b9 @bond:backbone  $atom:a9 $atom:a10
+    $bond:b10 @bond:backbone  $atom:a10 $atom:a11
+    $bond:b11 @bond:backbone  $atom:a11 $atom:a12
+    $bond:b12 @bond:backbone  $atom:a12 $atom:a13
+    $bond:b13 @bond:backbone  $atom:a13 $atom:a14
+    $bond:b14 @bond:backbone  $atom:a14 $atom:a15
+    $bond:b15 @bond:backbone  $atom:a15 $atom:a16
+    $bond:b16 @bond:backbone  $atom:a16 $atom:a17
+    $bond:b17 @bond:backbone  $atom:a17 $atom:a18
+    $bond:b18 @bond:backbone  $atom:a18 $atom:a19
+    $bond:b19 @bond:backbone  $atom:a19 $atom:a20
+    $bond:b20 @bond:backbone  $atom:a20 $atom:a21
+    $bond:b21 @bond:backbone  $atom:a21 $atom:a22
+    $bond:b22 @bond:backbone  $atom:a22 $atom:a23
+    $bond:b23 @bond:backbone  $atom:a23 $atom:a24
+    $bond:b24 @bond:backbone  $atom:a24 $atom:a25
+    $bond:b25 @bond:backbone  $atom:a25 $atom:a26
+    $bond:b26 @bond:backbone  $atom:a26 $atom:a27
+  }
+
+  # (3-body) Angles are specified below
+
+  # (4-body) Dihedrals must be defined explicitly for every quartet of atoms.
+  #          (These interactions are not determined by atom type.)
+
+  # dihedral-ID   dihedral-Type    atom-ID  atom-ID  atom-ID  atom-ID
+
+  write('Data Dihedrals') {
+
+    $dihedral:d1  @dihedral:beta  $atom:a1 $atom:a2 $atom:a3 $atom:a4
+    $dihedral:d2  @dihedral:beta  $atom:a2 $atom:a3 $atom:a4 $atom:a5
+    $dihedral:d3  @dihedral:beta  $atom:a3 $atom:a4 $atom:a5 $atom:a6
+    $dihedral:d4  @dihedral:beta  $atom:a4 $atom:a5 $atom:a6 $atom:a7
+
+    #    Dihedral angle forces in the turn regions were switched off
+    #    (in this model) so just I comment them out (and \ the variable names).
+    # \$dihedral:d5  \@dihedral:turn  $atom:a5 $atom:a6 $atom:a7 $atom:a8
+    # \$dihedral:d6  \@dihedral:turn  $atom:a6 $atom:a7 $atom:a8 $atom:a9
+    # \$dihedral:d7  \@dihedral:turn  $atom:a7 $atom:a8 $atom:a9 $atom:a10
+
+    $dihedral:d8  @dihedral:beta  $atom:a8 $atom:a9 $atom:a10 $atom:a11
+    $dihedral:d9  @dihedral:beta  $atom:a9 $atom:a10 $atom:a11 $atom:a12
+    $dihedral:d10  @dihedral:beta  $atom:a10 $atom:a11 $atom:a12 $atom:a13
+    $dihedral:d11  @dihedral:beta  $atom:a11 $atom:a12 $atom:a13 $atom:a14
+    $dihedral:d12  @dihedral:beta  $atom:a12 $atom:a13 $atom:a14 $atom:a15
+
+    #    Dihedral angle forces in the turn regions were switched off
+    #    (in this model) so just I comment them out (and \ the variable names).
+    # \$dihedral:d13  \@dihedral:turn  $atom:a13 $atom:a14 $atom:a15 $atom:a16
+    # \$dihedral:d14  \@dihedral:turn  $atom:a14 $atom:a15 $atom:a16 $atom:a17
+
+    $dihedral:d15  @dihedral:alpha  $atom:a15 $atom:a16 $atom:a17 $atom:a18
+    $dihedral:d16  @dihedral:alpha  $atom:a16 $atom:a17 $atom:a18 $atom:a19
+    $dihedral:d17  @dihedral:alpha  $atom:a17 $atom:a18 $atom:a19 $atom:a20
+    $dihedral:d18  @dihedral:alpha  $atom:a18 $atom:a19 $atom:a20 $atom:a21
+    $dihedral:d19  @dihedral:alpha  $atom:a19 $atom:a20 $atom:a21 $atom:a22
+    $dihedral:d20  @dihedral:alpha  $atom:a20 $atom:a21 $atom:a22 $atom:a23
+    $dihedral:d21  @dihedral:alpha  $atom:a21 $atom:a22 $atom:a23 $atom:a24
+    $dihedral:d22  @dihedral:alpha  $atom:a22 $atom:a23 $atom:a24 $atom:a25
+    $dihedral:d23  @dihedral:alpha  $atom:a23 $atom:a24 $atom:a25 $atom:a26
+    $dihedral:d24  @dihedral:alpha  $atom:a24 $atom:a25 $atom:a26 $atom:a27
+  }
+
+  # All consecutively bonded triplets of atoms same 3-body bond-angle 
+  # interaction parameters.  Of coarse, we could specify them all explicitly
+  # (as we did for the dihedrals above), but I wanted to show how to specify
+  # angles by atom type instead.  (You can do this for dihedrals & impropers
+  # also.)
+
+  #     angle-Type     atom-Type  atom-Type  atom-Type   bond-Type bond-Type
+
+  write_once('Data Angles By Type') {
+    @angle:backbone @atom:* @atom:* @atom:*  @bond:* @bond:*
+  }
+
+  # (The "*" is a wildcard character.  I use "*" to denote any atom-type or
+  #  bond-type which is defined within the current namespace: 1beadFrustrated)
+
+
+  # 2-body (non-bonded) interactions:
+  #
+  #   Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
+  #
+  #              i       j           pairstylename             eps      sig K L
+  #
+  write_once("In Settings") {
+    pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0          1.0 1 -1
+    pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0
+    pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0
+    pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1
+    pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25         1.0 1 0
+    pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0
+  }
+
+
+  # 2-body (bonded) interactions:
+  #
+  #   Ubond(r) = (k/2)*(r-0)^2
+  #
+  #   The corresponding command is:
+  #
+  #                  bond-Type   bondstylename     k    r0
+
+  write_once("In Settings") {
+    bond_coeff     @bond:backbone   harmonic    100.0  1.0
+  }
+
+  # 3-body interactions in this example are listed by atomType and bondType
+  # The atomIDs involved are determined automatically.  The forumula used is:
+  #
+  # Uangle(theta) = (k/2)*(theta-theta0)^2   
+  #     (k in kcal/mol/rad^2, theta0 in degrees)
+  #
+  #                 angle-Type   anglestylename    k         theta0
+
+  write_once("In Settings") {
+    angle_coeff    @angle:backbone  harmonic   13.3333333333  105.0
+  }
+
+
+  # We use tabular dihedral potentials to implement the dihedral forces.
+  # (Actually there is a way to use Fourier series, using multiple charmm 
+  #  style dihedral interactions, but it's slower and messier.)
+
+  write_once("In Settings") {
+    #                              style           file                 keyword
+    dihedral_coeff @dihedral:alpha table  table_dihedral_frustrated.dat FRUSTRATED_ALPHA
+    dihedral_coeff @dihedral:beta  table  table_dihedral_frustrated.dat FRUSTRATED_BETA
+    # No need to specify dihedral interactions in the turn regions. (none exist)
+  }
+
+  write_once("In Settings") {
+    # Optional: define the atoms in the "proteins" group
+    group proteins type @atom:B
+    group proteins type @atom:L
+    group proteins type @atom:N
+  }
+
+  # LAMMPS has many available force field styles (and atom styles). 
+  # Here, we pick the ones which work well for this molecular model:
+
+  write_once("In Init") {
+    # --- Default options for the "1BeadFrustrated" protein model ---
+    # ---            (These can be overridden later.)             ---
+    units           lj
+    atom_style      full
+    bond_style      hybrid harmonic
+    angle_style     hybrid harmonic
+    dihedral_style  hybrid table spline 360
+    pair_style      hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0
+    pair_modify     mix arithmetic
+    special_bonds   lj 0.0 0.0 1.0   #(turn on "1-4" interactions)
+  }
+
+} # 1beadFrustrated
+
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt

@@ -0,0 +1,85 @@
+import "1beadFrustrated.lt"
+
+
+# Alternate starting conformation (same molecule):
+
+
+1beadMisfolded inherits 1beadFrustrated {
+
+  # This molecule "inherits" all of its features from "1beadFrustrated".
+  # Here we override the atomic positions with new coordinates:
+
+  #  AtomID   MoleculeID AtomType  Charge       X        Y         Z
+
+  write("Data Atoms") {
+    $atom:a1   $mol   @atom:L    0.0   -0.69801399 -0.22114168 -1.9464876
+    $atom:a2   $mol   @atom:B    0.0   -0.40921658 -0.027063664 -1.0033251
+    $atom:a3   $mol   @atom:L    0.0   0.10259348 0.80836418 -1.0737085
+    $atom:a4   $mol   @atom:B    0.0   0.25857916 1.0054984 -0.11621451
+    $atom:a5   $mol   @atom:L    0.0   0.8258629 1.8325549 -0.18529135
+    $atom:a6   $mol   @atom:B    0.0   0.91366257 2.1950317 0.74175977
+    $atom:a7   $mol   @atom:N    0.0   1.4399539 1.554238 1.2994409
+    $atom:a8   $mol   @atom:N    0.0   0.73372573 1.0161012 1.7397275
+    $atom:a9   $mol   @atom:B    0.0   0.26608782 0.65302497 0.94353938
+    $atom:a10  $mol   @atom:L    0.0   0.97442305 0.13574211 0.50586398
+    $atom:a11  $mol   @atom:B    0.0   0.35889617 -0.18247555 -0.1764186
+    $atom:a12  $mol   @atom:L    0.0   0.87151735 -0.77260824 -0.75240916
+    $atom:a13  $mol   @atom:B    0.0   0.047726486 -1.0530682 -1.1902704
+    $atom:a14  $mol   @atom:L    0.0   0.34530697 -1.7476773 -1.8393331
+    $atom:a15  $mol   @atom:N    0.0   0.65865186 -2.45948 -1.2167056
+    $atom:a16  $mol   @atom:N    0.0   -0.16534524 -2.6219442 -0.67112167
+    $atom:a17  $mol   @atom:N    0.0   -0.010590421 -2.2445242 0.24748633
+    $atom:a18  $mol   @atom:B    0.0   0.18135771 -1.2564919 0.1767523
+    $atom:a19  $mol   @atom:B    0.0   -0.57472665 -0.82852797 -0.27027791
+    $atom:a20  $mol   @atom:L    0.0   -1.3967448 -1.0516787 0.24247346
+    $atom:a21  $mol   @atom:L    0.0   -1.003428 -0.85642681 1.1107555
+    $atom:a22  $mol   @atom:B    0.0   -0.25156735 -0.3182346 0.74262946
+    $atom:a23  $mol   @atom:B    0.0   -0.61751956 0.30115562 0.070426493
+    $atom:a24  $mol   @atom:L    0.0   -1.3347934 0.83310182 0.52625934
+    $atom:a25  $mol   @atom:L    0.0   -0.83315257 1.270904 1.2564086
+    $atom:a26  $mol   @atom:B    0.0   -0.10469759 1.6988523 0.72597181
+    $atom:a27  $mol   @atom:L    0.0   -0.57854905 2.3367737 0.11206868
+  }
+
+} # 1beadMisfolded
+
+
+1beadUnfolded inherits 1beadFrustrated {
+
+  # This molecule "inherits" all of its features from "1beadFrustrated"
+  # Here we override the atomic positions with new coordinates:
+
+  #  AtomID MoleculeID AtomType Charge   X        Y         Z
+
+  write('Data Atoms') {
+    $atom:a1   $mol   @atom:L    0.0    -2.4      1.7      -0.0
+    $atom:a2   $mol   @atom:B    0.0    -1.8      1.7       0.8
+    $atom:a3   $mol   @atom:L    0.0    -1.2      2.5       0.8
+    $atom:a4   $mol   @atom:B    0.0    -0.6      2.5      -0.0
+    $atom:a5   $mol   @atom:L    0.0     0.0      1.7      -0.0
+    $atom:a6   $mol   @atom:B    0.0     0.6      1.7       0.8
+    $atom:a7   $mol   @atom:N    0.0     1.2      2.5       0.8
+    $atom:a8   $mol   @atom:N    0.0     1.8      2.5      -0.0
+    $atom:a9   $mol   @atom:B    0.0     2.4      1.7      -0.0
+    $atom:a10  $mol   @atom:L    0.0     3.0      1.7      -0.8
+    $atom:a11  $mol   @atom:B    0.0     3.0      0.7      -0.8
+    $atom:a12  $mol   @atom:L    0.0     3.0      0.1      -0.0
+    $atom:a13  $mol   @atom:B    0.0     3.8     -0.5      -0.0
+    $atom:a14  $mol   @atom:L    0.0     3.8     -1.1      -0.8
+    $atom:a15  $mol   @atom:N    0.0     3.0     -1.7      -0.8
+    $atom:a16  $mol   @atom:N    0.0     3.0     -1.7       0.2
+    $atom:a17  $mol   @atom:N    0.0     2.4     -2.5       0.2
+    $atom:a18  $mol   @atom:B    0.0     1.8     -2.5      -0.6
+    $atom:a19  $mol   @atom:B    0.0     1.2     -1.7      -0.6
+    $atom:a20  $mol   @atom:L    0.0     0.6     -1.7       0.2
+    $atom:a21  $mol   @atom:L    0.0    -0.0     -2.5       0.2
+    $atom:a22  $mol   @atom:B    0.0    -0.6     -2.5      -0.6
+    $atom:a23  $mol   @atom:B    0.0    -1.2     -1.7      -0.6
+    $atom:a24  $mol   @atom:L    0.0    -1.8     -1.7       0.2
+    $atom:a25  $mol   @atom:L    0.0    -2.4     -2.5       0.2
+    $atom:a26  $mol   @atom:B    0.0    -3.0     -2.5      -0.6
+    $atom:a27  $mol   @atom:L    0.0    -3.6     -1.7      -0.6
+  }
+
+} # 1beadUnfolded
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py

@@ -0,0 +1,87 @@
+#!/usr/bin/env python
+
+# Calculate a table of pairwise energies and forces between atoms in the 
+# protein and a chaperone provided in the supplemental materials section of:
+# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
+# This is stored in a tabulated force field with a singularity at a distance R.
+#
+# To calculate the table for interaction between 
+# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table:
+#   ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181
+# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table:
+#   ./calc_chaperone_table.py 1.0 1.0 6.0 0.0   0.0 5.9 1181
+# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table:
+#   ./calc_chaperone_table.py 1.0 1.0 3.0 0.60  3.1 8.0 981 True
+# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table:
+#   ./calc_chaperone_table.py 1.0 1.0 3.0 0.0   3.1 8.0 981 True
+
+from math import *
+import sys
+
+def U(r, eps, sigma, R, h):
+    #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h))
+    # Formula is undefined at r=0, but you can take the limit:
+    if r <= 0:
+        return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0)
+                               - h*pow((sigma/R), 6.0))
+    xp = sigma/(r+R)
+    xm = sigma/(r-R)
+    term10 = pow(xm, 10.0) - pow(xp, 10.0)
+    term4  = pow(xm, 4.0)  - pow(xp, 4.0)
+    return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4)
+
+def F(r, eps, sigma, R, h):
+    # Formula is undefined at r=0, but you can take the limit:
+    if r <= 0:
+        return 0.0
+    product_term_a = U(r, eps, sigma, R, h) / r
+    ixp = (r+R)/sigma
+    ixm = (r-R)/sigma
+    dix_dr = 1.0/sigma
+    term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0))
+    term4  =  (4.0/sigma)*(pow(ixm, -5.0)  - pow(ixp, -5.0))
+    product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4)
+    return product_term_a + product_term_b
+    
+
+class InputError(Exception):
+    """ A generic exception object containing a string for error reporting.
+
+    """
+    def __init__(self, err_msg):
+        self.err_msg = err_msg
+    def __str__(self):
+        return self.err_msg
+    def __repr__(self):
+        return str(self)
+
+if len(sys.argv) < 8:
+    sys.stderr.write("Error: expected 7 arguments:\n"
+                     "\n"
+                     "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n")
+    sys.exit(-1)
+
+epsilon = float(sys.argv[1])
+sigma   = float(sys.argv[2])
+R       = float(sys.argv[3])
+h       = float(sys.argv[4])
+rmin    = float(sys.argv[5])
+rmax    = float(sys.argv[6])
+N       = int(sys.argv[7])
+
+subtract_Urcut = False
+if len(sys.argv) == 9:
+    subtract_Urcut = True
+rcut    = rmax
+
+for i in range(0,N):
+    r = rmin + i*(rmax-rmin)/(N-1)
+    U_r = U(r, epsilon, sigma, R, h) 
+    F_r = F(r, epsilon, sigma, R, h)
+    if subtract_Urcut:
+        U_r -= U(rcut, epsilon, sigma, R, h)
+        if (r >= rcut) or (i==N-1):
+            U_r = 0.0
+            F_r = 0.0
+    print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py

@@ -0,0 +1,67 @@
+#!/usr/bin/env python
+
+# Calculate a table of dihedral angle interactions used in the alpha-helix
+# and beta-sheet regions of the frustrated protein model described in
+#  provided in figure 8 of the supplemental materials section of:
+# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
+# Note that the "A" and "B" parameters were incorrectly reported to be 
+# 5.4*epsilon and 6.0*epsilon.  The values used were 5.6 and 6.0 epsilon.
+# The phiA and phiB values were 57.29577951308232 degrees (1 rad) 
+# and 180 degrees, respectively.  Both expA and expB were 6.0.
+#
+# To generate the table used for the alpha-helix (1 degree resolution) use this:
+#  ./calc_dihedral_table.py 6.0 57.29577951308232 6  5.6 180 6  0.0 359  360
+# To generate the table used for the beta-sheets (1 degree resolution) use this:
+#  ./calc_dihedral_table.py 5.6 57.29577951308232 6  6.0 180 6  0.0 359  360
+#
+# (If you're curious as to why I set the location of the minima at phi_alpha
+#  to 1.0 radians (57.2957795 degrees), there was no particularly good reason.
+#  I think the correct value turns out to be something closer to 50 degrees.)
+
+
+from math import *
+import sys
+
+
+# The previous version included the repulsive core term
+def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
+    conv_units = pi/180.0
+    if use_radians:
+        conv_units = 1.0
+    termA = pow(cos(0.5*(phi-phiA)*conv_units), expA)
+    termB = pow(cos(0.5*(phi-phiB)*conv_units), expB)
+    return -A*termA - B*termB
+
+# The previous version included the repulsive core term
+def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
+    conv_units = pi/180.0
+    if use_radians:
+        conv_units = 1.0
+    termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * 
+             expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0))
+    termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * 
+             expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0))
+    return -conv_units*(A*termA + B*termB)
+
+if len(sys.argv) != 10:
+    sys.stderr.write("Error: expected 9 arguments:\n"
+                     "\n"
+                     "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n")
+    sys.exit(-1)
+
+A       = float(sys.argv[1])
+phiA    = float(sys.argv[2])
+expA    = float(sys.argv[3])
+B       = float(sys.argv[4])
+phiB    = float(sys.argv[5])
+expB    = float(sys.argv[6])
+phi_min = float(sys.argv[7])
+phi_max = float(sys.argv[8])
+N       =   int(sys.argv[9])
+
+for i in range(0,N):
+    phi = phi_min + i*(phi_max - phi_min)/(N-1)
+    U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
+    F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
+    print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi))
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt

@@ -0,0 +1,41 @@
+# Here we define a trivial molecule containing only one particle.
+
+Minichaperone {
+
+  # atomID molID atomType charge   x  y  z
+
+  write("Data Atoms") {
+    $atom:C $mol @atom:C   0.0   0.0 0.0 0.0
+  }
+
+  write_once("Data Masses") {
+    @atom:C 100.0
+  }
+
+  write_once("In Settings") {
+    # If for some reason there are multiple chaperones present, 
+    # I assume that they interact repulsively (hence, L=0)
+
+    #            i     j        pairStyle                   eps sig K L
+
+    pair_coeff @atom:C @atom:C  lj/charmm/coul/charmm/inter 1.0 3.0 1 0
+
+    # Optional: define the atoms in the "chaperonins" group:
+    # (Defining a group for the chaperone makes it easy to immobilize it later.)
+
+    group chaperones type @atom:C
+  }
+
+  # Specify which pair_styles, and atom styles work well with 
+  # this model.  (Again this can be overridden later.)
+
+  write_once("In Init") {
+    units       lj
+    atom_style  full
+    pair_style  hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 8.0 9.0
+  }
+
+} # Minichaperone
+
+# We have not specified how this particle interacts with other particles
+# besides itself.  Later on you must do this.

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt

@@ -0,0 +1,72 @@
+write_once("Data Boundary") {
+  0.0  80.0  xlo xhi
+  0.0  80.0  ylo yhi
+  0.0  80.0  zlo zhi
+}
+
+
+import "1beadFrustrated_variants.lt"
+import "minichaperone.lt"
+
+
+# Create 8 proteins and 8 chaperones (2x2x2 array):
+# NOTE: Below I create multiple proteins and multiple chaperones
+#       to see what would happen. (I suspect nothing good.  In the
+#       2006 paper, only 1 protein and 1 chaperone were present.)
+
+
+proteins   = new 1beadUnfolded [2].move(40,0,0)
+                               [2].move(0,40,0)
+                               [2].move(0,0,40)
+
+chaperones = new Minichaperone [2].move(40,0,0)
+                               [2].move(0,40,0)
+                               [2].move(0,0,40)
+
+proteins[*][*][*].move(20,20,20)  # to avoid overlap with the chaperones
+
+
+
+#    If you only want 1 protein and 1 chaperone
+#    then replace the lines above with:
+#
+# protein   = new 1beadMisfolded
+# chaperone = new Minichaperone
+
+
+
+
+
+# ---- Now define interactions between the atoms in the protein ----
+# ---- (named "B", "L", "N") and the atom which represents the  ----
+# ---- chaperone ("c").  These interactions are tabulated.      ----
+
+write_once("In Settings") {
+  pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/B  table  table_minichaperone_h=0.6.dat CH_H0.6
+  pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/L  table  table_minichaperone_h=0.dat   CH_H0
+  pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/N  table  table_minichaperone_h=0.dat   CH_H0
+}
+
+# Note: If you want purely repulsive spheres (crowding, h=0.0)
+#       instead of an attractive "hydrophobic" chaperone (h=0.6)
+#       then replace "table_minichaperone_h=0_6.dat CH_H0_6"
+#       with "table_minichaperone_h=0.dat CH_H0"
+#       (... or just use an ordinary Lennard-Jones interaction
+#            with sigma = 6.0 and epsilon near 0.0)
+
+
+# LAMMPS has many available force field styles (and atom styles).  Here we
+# select the ones which work well for the full combine system.  (This should 
+# override any settings made in "1beadFrustrated.lt" or "minichaperone.lt")
+
+
+write_once("In Init") {
+  units           lj
+  atom_style      full
+  bond_style      hybrid harmonic
+  angle_style     hybrid harmonic
+  dihedral_style  hybrid table spline 360
+  pair_style      hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 981
+  pair_modify     mix arithmetic
+  special_bonds   lj 0.0 0.0 1.0   #(turn on "1-4" interactions)
+}

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat

@@ -0,0 +1,735 @@
+# Table of the potential and its negative derivative for frustrated alpha helix
+# (Note: Derivatives are in units of energy/radians, not energy/degrees.)
+# ./calc_dihedral_table.py 6.0 57.29577951308232 6  5.6 180 6  0.0 359  360
+
+FRUSTRATED_ALPHA
+N 360 DEGREES
+
+1 0.0 -2.74081145103 0.0783990792662
+2 1.0 -2.81950869101 0.0789852583442
+3 2.0 -2.89876136749 0.0795096391909
+4 3.0 -2.97850675562 0.0799703813963
+5 4.0 -3.05868032959 0.0803657243943
+6 5.0 -3.13921584545 0.0806939935737
+7 6.0 -3.22004543014 0.0809536062381
+8 7.0 -3.30109967628 0.0811430773977
+9 8.0 -3.38230774267 0.0812610253741
+10 9.0 -3.46359746038 0.0813061772009
+11 10.0 -3.54489544401 0.0812773738039
+12 11.0 -3.62612720812 0.0811735749433
+13 12.0 -3.70721728841 0.0809938639029
+14 13.0 -3.78808936748 0.080737451911
+15 14.0 -3.86866640485 0.0804036822781
+16 15.0 -3.94887077101 0.0799920342374
+17 16.0 -4.02862438516 0.0795021264757
+18 17.0 -4.10784885622 0.0789337203415
+19 18.0 -4.18646562704 0.0782867227197
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+22 21.0 -4.41788477419 0.0758754834523
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+
+# Table of the potential and its negative derivative for frustrated beta sheet
+# (Note: Derivatives are in units of energy/radians, not energy/degrees.)
+#  ./calc_dihedral_table.py 5.6 57.29577951308232 6  6.0 180 6  0.0 359  360
+
+FRUSTRATED_BETA
+N 360 DEGREES
+
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tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat

@@ -0,0 +1,988 @@
+# Interaction between a chaperone wall and hydrophobic ("B") beads (h=0.6)
+# Generated using:
+# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True
+
+CH_H0.6
+N 981 R 3.1 8.0
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tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat

@@ -0,0 +1,989 @@
+# Interaction between a chaperone wall and hydrophilic ("L", "N") beads (h=0.0)
+# Generated using:
+# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.00 3.1 8.0 981 True
+
+CH_H0
+N 981 R 3.1 8.0
+
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+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min

@@ -0,0 +1,24 @@
+# -- Init section --
+
+include system.in.init
+
+# -- Atom definition section --
+
+read_data system.data
+
+# -- Settings Section --
+
+include system.in.settings
+
+# Optional: Make sure the pairwise energies look reasonable:
+pair_write 1 4 1001 r 4.05 8 test_chap-B.dat C-B 0 0
+pair_write 2 4 1001 r 4.05 8 test_chap-L.dat C-L 0 0
+pair_write 3 4 1001 r 4.05 8 test_chap-N.dat C-N 0 0
+
+# -- Run section --
+
+dump            1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
+
+minimize 1.0e-5 1.0e-7 500 2000
+
+write_restart  system_after_min.rst

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt

@@ -0,0 +1,46 @@
+# -- Init Section --
+
+include system.in.init
+
+# -- Atom Definition Section --
+
+# I you want to be careful, you can minimize the system first.  (Try using 
+# "run.in.min" and uncomment the read_restart command in this file below.)
+# read_restart system_after_min.rst
+
+read_data system.data
+
+# -- Settings Section --
+
+include system.in.settings
+
+# -- Run Section --
+
+
+timestep        0.025
+dump            1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz
+
+# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve".
+# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
+
+fix fxlan all langevin 0.25 0.25 1.0 48279
+fix fxnve all nve
+
+# Notes:
+# The temperature is in reduced units and is set to 0.25
+# which is the folding temperature for the frustrated protein
+# The inverse-damping-rate "damp" (which has units of time) is set to 1.0,
+# as it was in the paper.  (Hopefully folding times should be similar.)
+# (See http://lammps.sandia.gov/doc/fix_langevin.html)
+
+
+thermo_style    custom step temp pe etotal press vol epair ebond eangle edihed
+thermo_modify   norm no  #(report total energy not energy / num_atoms)
+thermo          5000     #(time interval for printing out "thermo" data)
+
+#restart         100000000  restart_nvt
+
+run		1000000000
+
+write_restart  system_after_nvt.rst
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT

@@ -0,0 +1,29 @@
+# This directory demonstrates how to run a short simulation of 
+# the "frustrated" coarse-grained protein model used in:
+# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
+# (http://www.pnas.org/content/101/36/13192)
+#
+# During this short simulation (run_short_sim.nvt.in) the protein evolves 
+# from an unfolded initial conformation to a misfolded conformation.
+# (Visualize using VMD.  Note: It can take hundreds of millions of 
+#  timesteps to escape from this conformation and reach the folded state.)
+#
+# -------- REQUIREMENTS: ---------
+# 1) This example requires the "USER-MISC" package.  (Use "make yes-USER-MISC")
+#   http://lammps.sandia.gov/doc/Section_start.html#start_3
+# 2) It also may require additional features and bug fixes for LAMMPS.
+#   be sure to download and copy the "additional_lammps_code" from 
+#   http://moltemplate.org     (upper-left corner menu)
+# 3) Unpack it
+# 4) copy the .cpp and .h files to the src folding of your lammps installation.
+# 5) Compile LAMMPS.
+
+-------------
+Instructions on how to build LAMMPS input files and 
+run a short simulation are provided in other README files.
+
+step 1)
+README_setup.sh
+
+step2)
+README_run.sh

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh

@@ -0,0 +1,21 @@
+# You would probably run lammps this way:
+#
+# lmp_ubuntu -i run.in.nvt
+
+# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer
+# to the input scripts & data files you created earlier when you ran moltemplate
+# system.in.init, system.in.settings, system.data
+
+
+# -----------------------------------
+
+LAMMPS_COMMAND="lmp_ubuntu"
+
+# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
+# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary.
+
+# Run lammps using the following 3 commands:
+
+"$LAMMPS_COMMAND" -i run.in.min              # minimize         (OPTIONAL)
+"$LAMMPS_COMMAND" -i run_short_sim.in.nvt    # production run
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh

@@ -0,0 +1,24 @@
+# Use these commands to generate the LAMMPS input script and data file
+# (and other auxilliary files):
+
+
+# Create LAMMPS input files this way:
+cd moltemplate_files
+
+  # run moltemplate
+
+  moltemplate.sh -overlay-dihdedrals system.lt
+
+  # This will generate various files with names ending in *.in* and *.data. 
+  # These files are the input files directly read by LAMMPS.  Move them to 
+  # the parent directory (or wherever you plan to run the simulation).
+
+  mv -f system.in* system.data ../
+  cp -r table*.dat ../
+
+  # Optional:
+  # The "./output_ttree/" directory is full of temporary files generated by 
+  # moltemplate.  They can be useful for debugging, but are usually thrown away.
+  rm -rf output_ttree/
+
+cd ../

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt

@@ -0,0 +1,87 @@
+
+ ------- To view a lammps trajectory in VMD --------
+
+
+1) Build a PSF file for use in viewing with VMD.
+
+This step works with VMD 1.9 and topotools 1.2.  
+(Older versions, like VMD 1.8.6, don't support this.)
+
+
+a) Start VMD
+b) Menu  Extensions->Tk Console
+c) Enter:
+
+(I assume that the the DATA file is called "system.data")
+
+   topo readlammpsdata system.data full
+   animate write psf system.psf
+
+2) 
+
+Later, to Load a trajectory in VMD:
+
+  Start VMD
+  Select menu: File->New Molecule
+ -Browse to select the PSF file you created above, and load it.
+  (Don't close the window yet.)
+ -Browse to select the trajectory file.
+  If necessary, for "file type" select: "LAMMPS Trajectory"
+  Load it.
+
+   ----  A note on trajectory format: -----
+If the trajectory is a DUMP file, then make sure the it contains the
+information you need for pbctools (see below.  I've been using this 
+command in my LAMMPS scripts to create the trajectories:
+
+  dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
+
+It's a good idea to use an atom_style which supports molecule-ID numbers 
+so that you can assign a molecule-ID number to each atom.  (I think this 
+is needed to wrap atom coordinates without breaking molecules in half.)
+
+Of course, you don't have to save your trajectories in DUMP format, 
+(other formats like DCD work fine)  I just mention dump files 
+because these are the files I'm familiar with.
+
+3) -----  Wrap the coordinates to the unit cell
+          (without cutting the molecules in half)
+
+a) Start VMD
+b) Load the trajectory in VMD (see above)
+c) Menu  Extensions->Tk Console
+d) Try entering these commands:
+
+    pbc wrap -compound res -all
+    pbc box
+
+    ----- Optional ----
+    Sometimes the solvent or membrane obscures the view of the solute.
+    It can help to shift the location of the periodic boundary box 
+    To shift the box in the y direction (for example) do this:
+
+    pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
+    pbc box -shiftcenterrel {0.0 0.15 0.0}
+
+    Distances are measured in units of box-length fractions, not Angstroms.
+
+    Alternately if you have a solute whose atoms are all of type 1, 
+    then you can also try this to center the box around it:
+
+    pbc wrap -sel type=1 -all -centersel type=2 -center com
+
+4) 
+    You should check if your periodic boundary conditions are too small.
+    To do that:
+       select Graphics->Representations menu option
+       click on the "Periodic" tab, and 
+       click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
+
+5) Optional: If you like, change the atom types in the PSF file so 
+   that VMD recognizes the atom types, use something like:
+
+sed -e 's/   1    1      /   C    C      /g' < system.psf > temp1.psf
+sed -e 's/   2    2      /   H    H      /g' < temp1.psf  > temp2.psf
+sed -e 's/   3    3      /   P    P      /g' < temp2.psf  > system.psf
+
+(If you do this, it might effect step 2 above.)

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf

@@ -0,0 +1,85 @@
+PSF
+
+       1 !NTITLE
+ REMARKS VMD generated structure x-plor psf file
+
+      27 !NATOM
+       1      1         2    2      0.000000        1.0000           0
+       2      1         1    1      0.000000        1.0000           0
+       3      1         2    2      0.000000        1.0000           0
+       4      1         1    1      0.000000        1.0000           0
+       5      1         2    2      0.000000        1.0000           0
+       6      1         1    1      0.000000        1.0000           0
+       7      1         3    3      0.000000        1.0000           0
+       8      1         3    3      0.000000        1.0000           0
+       9      1         1    1      0.000000        1.0000           0
+      10      1         2    2      0.000000        1.0000           0
+      11      1         1    1      0.000000        1.0000           0
+      12      1         2    2      0.000000        1.0000           0
+      13      1         1    1      0.000000        1.0000           0
+      14      1         2    2      0.000000        1.0000           0
+      15      1         3    3      0.000000        1.0000           0
+      16      1         3    3      0.000000        1.0000           0
+      17      1         3    3      0.000000        1.0000           0
+      18      1         1    1      0.000000        1.0000           0
+      19      1         1    1      0.000000        1.0000           0
+      20      1         2    2      0.000000        1.0000           0
+      21      1         2    2      0.000000        1.0000           0
+      22      1         1    1      0.000000        1.0000           0
+      23      1         1    1      0.000000        1.0000           0
+      24      1         2    2      0.000000        1.0000           0
+      25      1         2    2      0.000000        1.0000           0
+      26      1         1    1      0.000000        1.0000           0
+      27      1         2    2      0.000000        1.0000           0
+
+      26 !NBOND: bonds
+       1       2       2       3       3       4       4       5
+       5       6       6       7       7       8       8       9
+       9      10      10      11      11      12      12      13
+      13      14      14      15      15      16      16      17
+      17      18      18      19      19      20      20      21
+      21      22      22      23      23      24      24      25
+      25      26      26      27
+
+      25 !NTHETA: angles
+      13      14      15       7       8       9       6       7       8
+      16      17      18      15      16      17       2       3       4
+       4       5       6       9      10      11      11      12      13
+      14      15      16       1       2       3       3       4       5
+      10      11      12      12      13      14      25      26      27
+       5       6       7       8       9      10      17      18      19
+      18      19      20      22      23      24      21      22      23
+      19      20      21      20      21      22      23      24      25
+      24      25      26
+
+      19 !NPHI: dihedrals
+       1       2       3       4       2       3       4       5
+       3       4       5       6       4       5       6       7
+       8       9      10      11       9      10      11      12
+      10      11      12      13      11      12      13      14
+      12      13      14      15      15      16      17      18
+      16      17      18      19      17      18      19      20
+      18      19      20      21      19      20      21      22
+      20      21      22      23      21      22      23      24
+      22      23      24      25      23      24      25      26
+      24      25      26      27
+
+       0 !NIMPHI: impropers
+
+
+       0 !NDON: donors
+
+
+       0 !NACC: acceptors
+
+
+       0 !NNB
+
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0
+
+       1       0 !NGRP
+       0       0       0
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt

@@ -0,0 +1,216 @@
+# This file defines the "frustrated" coarse-grained protein model used in:
+# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
+# (http://www.pnas.org/content/101/36/13192)
+
+
+1beadFrustrated {
+
+  # There are 3 atom types (referred to above as B, L, and N)
+  # Define their masses:
+
+  write_once("Data Masses") {
+    @atom:B   1.0
+    @atom:L   1.0
+    @atom:N   1.0
+  }
+
+  #  AtomID  MoleculeID  AtomType  Charge  X        Y         Z
+
+  write("Data Atoms") {
+    $atom:a1  $mol  @atom:L  0.0   -0.92636654 -1.8409904 -2.1482679
+    $atom:a2  $mol  @atom:B  0.0   -0.57313354 -1.0670787 -1.6182341
+    $atom:a3  $mol  @atom:L  0.0   -0.85707399 -1.2358703 -0.69350966
+    $atom:a4  $mol  @atom:B  0.0   -0.44231274 -0.4584993 -0.23418709
+    $atom:a5  $mol  @atom:L  0.0   -0.75081182 -0.62868078 0.69786737
+    $atom:a6  $mol  @atom:B  0.0   -0.36201977 0.11619615 1.2249098
+    $atom:a7  $mol  @atom:N  0.0   -0.63708237 -0.15973084 2.1723919
+    $atom:a8  $mol  @atom:N  0.0   0.20516047 0.10417157 2.624901
+    $atom:a9  $mol  @atom:B  0.0   0.57223743 0.44728103 1.7695617
+    $atom:a10 $mol  @atom:L  0.0   0.77646279 -0.40630393 1.3168043
+    $atom:a11 $mol  @atom:B  0.0   0.45475664 -0.2077937 0.40045721
+    $atom:a12 $mol  @atom:L  0.0   0.72712495 -1.0397637 -0.087614951
+    $atom:a13 $mol  @atom:B  0.0   0.36971183 -0.85840501 -0.9933019
+    $atom:a14 $mol  @atom:L  0.0   0.74784336 -1.5700415 -1.5859217
+    $atom:a15 $mol  @atom:N  0.0   0.43423905 -1.2758917 -2.4853429
+    $atom:a16 $mol  @atom:N  0.0   0.70583191 -0.30726921 -2.4987711
+    $atom:a17 $mol  @atom:N  0.0   -0.091688915 0.23323014 -2.2051358
+    $atom:a18 $mol  @atom:B  0.0   -0.34243283 -0.035822049 -1.2644719
+    $atom:a19 $mol  @atom:B  0.0   0.41961247 0.18475451 -0.65971014
+    $atom:a20 $mol  @atom:L  0.0   0.51968465 1.1546791 -0.77877053
+    $atom:a21 $mol  @atom:L  0.0   -0.40827985 1.2765273 -0.52550748
+    $atom:a22 $mol  @atom:B  0.0   -0.368141 0.58090904 0.19152224
+    $atom:a23 $mol  @atom:B  0.0   0.40327249 0.86101769 0.7336255
+    $atom:a24 $mol  @atom:L  0.0   0.22707289 1.8326235 0.89673346
+    $atom:a25 $mol  @atom:L  0.0   -0.66500182 1.7285809 1.2783166
+    $atom:a26 $mol  @atom:B  0.0   -0.39205603 1.0475436 1.9328097
+    $atom:a27 $mol  @atom:L  0.0   0.25339027 1.5246265 2.5388463
+  }
+
+  # bond-ID   bond-Type      atom-ID  atom-ID
+
+  write("Data Bonds") {
+    $bond:b1 @bond:backbone  $atom:a1 $atom:a2
+    $bond:b2 @bond:backbone  $atom:a2 $atom:a3
+    $bond:b3 @bond:backbone  $atom:a3 $atom:a4
+    $bond:b4 @bond:backbone  $atom:a4 $atom:a5
+    $bond:b5 @bond:backbone  $atom:a5 $atom:a6
+    $bond:b6 @bond:backbone  $atom:a6 $atom:a7
+    $bond:b7 @bond:backbone  $atom:a7 $atom:a8
+    $bond:b8 @bond:backbone  $atom:a8 $atom:a9
+    $bond:b9 @bond:backbone  $atom:a9 $atom:a10
+    $bond:b10 @bond:backbone  $atom:a10 $atom:a11
+    $bond:b11 @bond:backbone  $atom:a11 $atom:a12
+    $bond:b12 @bond:backbone  $atom:a12 $atom:a13
+    $bond:b13 @bond:backbone  $atom:a13 $atom:a14
+    $bond:b14 @bond:backbone  $atom:a14 $atom:a15
+    $bond:b15 @bond:backbone  $atom:a15 $atom:a16
+    $bond:b16 @bond:backbone  $atom:a16 $atom:a17
+    $bond:b17 @bond:backbone  $atom:a17 $atom:a18
+    $bond:b18 @bond:backbone  $atom:a18 $atom:a19
+    $bond:b19 @bond:backbone  $atom:a19 $atom:a20
+    $bond:b20 @bond:backbone  $atom:a20 $atom:a21
+    $bond:b21 @bond:backbone  $atom:a21 $atom:a22
+    $bond:b22 @bond:backbone  $atom:a22 $atom:a23
+    $bond:b23 @bond:backbone  $atom:a23 $atom:a24
+    $bond:b24 @bond:backbone  $atom:a24 $atom:a25
+    $bond:b25 @bond:backbone  $atom:a25 $atom:a26
+    $bond:b26 @bond:backbone  $atom:a26 $atom:a27
+  }
+
+  # (3-body) Angles are specified below
+
+  # (4-body) Dihedrals must be defined explicitly for every quartet of atoms.
+  #          (These interactions are not determined by atom type.)
+
+  # dihedral-ID   dihedral-Type    atom-ID  atom-ID  atom-ID  atom-ID
+
+  write("Data Dihedrals") {
+
+    $dihedral:d1  @dihedral:beta  $atom:a1 $atom:a2 $atom:a3 $atom:a4
+    $dihedral:d2  @dihedral:beta  $atom:a2 $atom:a3 $atom:a4 $atom:a5
+    $dihedral:d3  @dihedral:beta  $atom:a3 $atom:a4 $atom:a5 $atom:a6
+    $dihedral:d4  @dihedral:beta  $atom:a4 $atom:a5 $atom:a6 $atom:a7
+
+    #    Dihedral angle forces in the turn regions were switched off
+    #    (in this model) so just I comment them out (and \ the variable names).
+    # \$dihedral:d5  \@dihedral:turn  $atom:a5 $atom:a6 $atom:a7 $atom:a8
+    # \$dihedral:d6  \@dihedral:turn  $atom:a6 $atom:a7 $atom:a8 $atom:a9
+    # \$dihedral:d7  \@dihedral:turn  $atom:a7 $atom:a8 $atom:a9 $atom:a10
+
+    $dihedral:d8  @dihedral:beta  $atom:a8 $atom:a9 $atom:a10 $atom:a11
+    $dihedral:d9  @dihedral:beta  $atom:a9 $atom:a10 $atom:a11 $atom:a12
+    $dihedral:d10  @dihedral:beta  $atom:a10 $atom:a11 $atom:a12 $atom:a13
+    $dihedral:d11  @dihedral:beta  $atom:a11 $atom:a12 $atom:a13 $atom:a14
+    $dihedral:d12  @dihedral:beta  $atom:a12 $atom:a13 $atom:a14 $atom:a15
+
+    #    Dihedral angle forces in the turn regions were switched off
+    #    (in this model) so just I comment them out (and \ the variable names).
+    # \$dihedral:d13  \@dihedral:turn  $atom:a13 $atom:a14 $atom:a15 $atom:a16
+    # \$dihedral:d14  \@dihedral:turn  $atom:a14 $atom:a15 $atom:a16 $atom:a17
+
+    $dihedral:d15  @dihedral:alpha  $atom:a15 $atom:a16 $atom:a17 $atom:a18
+    $dihedral:d16  @dihedral:alpha  $atom:a16 $atom:a17 $atom:a18 $atom:a19
+    $dihedral:d17  @dihedral:alpha  $atom:a17 $atom:a18 $atom:a19 $atom:a20
+    $dihedral:d18  @dihedral:alpha  $atom:a18 $atom:a19 $atom:a20 $atom:a21
+    $dihedral:d19  @dihedral:alpha  $atom:a19 $atom:a20 $atom:a21 $atom:a22
+    $dihedral:d20  @dihedral:alpha  $atom:a20 $atom:a21 $atom:a22 $atom:a23
+    $dihedral:d21  @dihedral:alpha  $atom:a21 $atom:a22 $atom:a23 $atom:a24
+    $dihedral:d22  @dihedral:alpha  $atom:a22 $atom:a23 $atom:a24 $atom:a25
+    $dihedral:d23  @dihedral:alpha  $atom:a23 $atom:a24 $atom:a25 $atom:a26
+    $dihedral:d24  @dihedral:alpha  $atom:a24 $atom:a25 $atom:a26 $atom:a27
+  }
+
+  # All consecutively bonded triplets of atoms same 3-body bond-angle 
+  # interaction parameters.  Of coarse, we could specify them all explicitly
+  # (as we did for the dihedrals above), but I wanted to show how to specify
+  # angles by atom type instead.  (You can do this for dihedrals & impropers
+  # also.)
+
+  #     angle-Type     atom-Type  atom-Type  atom-Type   bond-Type bond-Type
+
+  write_once("Data Angles By Type") {
+    @angle:backbone @atom:* @atom:* @atom:*  @bond:* @bond:*
+  }
+
+  # (The "*" is a wildcard character.  I use "*" to denote any atom-type or
+  #  bond-type which is defined within the current namespace: 1beadFrustrated)
+
+
+  # 2-body (non-bonded) interactions:
+  #
+  #   Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
+  #
+  #              i       j           pairstylename             eps      sig K L
+  #
+  write_once("In Settings") {
+    pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0          1.0 1 -1
+    pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0
+    pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0
+    pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1
+    pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25         1.0 1 0
+    pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0
+  }
+
+
+  # 2-body (bonded) interactions:
+  #
+  #   Ubond(r) = (k/2)*(r-0)^2
+  #
+  #   The corresponding command is:
+  #
+  #                  bond-Type   bondstylename     k    r0
+
+  write_once("In Settings") {
+    bond_coeff     @bond:backbone   harmonic    100.0  1.0
+  }
+
+  # 3-body interactions in this example are listed by atomType and bondType
+  # The atomIDs involved are determined automatically.  The forumula used is:
+  #
+  # Uangle(theta) = (k/2)*(theta-theta0)^2   
+  #     (k in kcal/mol/rad^2, theta0 in degrees)
+  #
+  #                 angle-Type   anglestylename    k         theta0
+
+  write_once("In Settings") {
+    angle_coeff    @angle:backbone  harmonic   13.3333333333  105.0
+  }
+
+
+  # We use tabular dihedral potentials to implement the dihedral forces.
+  # (Actually there is a way to use Fourier series, using multiple charmm 
+  #  style dihedral interactions, but it's slower and messier.)
+
+  write_once("In Settings") {
+    #                              style           file                 keyword
+    dihedral_coeff @dihedral:alpha table  table_dihedral_frustrated.dat FRUSTRATED_ALPHA
+    dihedral_coeff @dihedral:beta  table  table_dihedral_frustrated.dat FRUSTRATED_BETA
+    # No need to specify dihedral interactions in the turn regions. (none exist)
+  }
+
+  write_once("In Settings") {
+    # Optional: define the atoms in the "proteins" group
+    group proteins type @atom:B
+    group proteins type @atom:L
+    group proteins type @atom:N
+  }
+
+  # LAMMPS has many available force field styles (and atom styles). 
+  # Here, we pick the ones which work well for this molecular model:
+
+  write_once("In Init") {
+    # --- Default options for the "1BeadFrustrated" protein model ---
+    # ---            (These can be overridden later.)             ---
+    units           lj
+    atom_style      full
+    bond_style      hybrid harmonic
+    angle_style     hybrid harmonic
+    dihedral_style  hybrid table spline 360
+    pair_style      hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0
+    pair_modify     mix arithmetic
+    special_bonds   lj 0.0 0.0 1.0   #(turn on "1-4" interactions)
+  }
+
+} # 1beadFrustrated
+
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt

@@ -0,0 +1,85 @@
+import "1beadFrustrated.lt"
+
+
+# Alternate starting conformation (same molecule):
+
+
+1beadMisfolded inherits 1beadFrustrated {
+
+  # This molecule "inherits" all of its features from "1beadFrustrated".
+  # Here we override the atomic positions with new coordinates:
+
+  #  AtomID   MoleculeID AtomType  Charge       X        Y         Z
+
+  write("Data Atoms") {
+    $atom:a1   $mol   @atom:L    0.0   -0.69801399 -0.22114168 -1.9464876
+    $atom:a2   $mol   @atom:B    0.0   -0.40921658 -0.027063664 -1.0033251
+    $atom:a3   $mol   @atom:L    0.0   0.10259348 0.80836418 -1.0737085
+    $atom:a4   $mol   @atom:B    0.0   0.25857916 1.0054984 -0.11621451
+    $atom:a5   $mol   @atom:L    0.0   0.8258629 1.8325549 -0.18529135
+    $atom:a6   $mol   @atom:B    0.0   0.91366257 2.1950317 0.74175977
+    $atom:a7   $mol   @atom:N    0.0   1.4399539 1.554238 1.2994409
+    $atom:a8   $mol   @atom:N    0.0   0.73372573 1.0161012 1.7397275
+    $atom:a9   $mol   @atom:B    0.0   0.26608782 0.65302497 0.94353938
+    $atom:a10  $mol   @atom:L    0.0   0.97442305 0.13574211 0.50586398
+    $atom:a11  $mol   @atom:B    0.0   0.35889617 -0.18247555 -0.1764186
+    $atom:a12  $mol   @atom:L    0.0   0.87151735 -0.77260824 -0.75240916
+    $atom:a13  $mol   @atom:B    0.0   0.047726486 -1.0530682 -1.1902704
+    $atom:a14  $mol   @atom:L    0.0   0.34530697 -1.7476773 -1.8393331
+    $atom:a15  $mol   @atom:N    0.0   0.65865186 -2.45948 -1.2167056
+    $atom:a16  $mol   @atom:N    0.0   -0.16534524 -2.6219442 -0.67112167
+    $atom:a17  $mol   @atom:N    0.0   -0.010590421 -2.2445242 0.24748633
+    $atom:a18  $mol   @atom:B    0.0   0.18135771 -1.2564919 0.1767523
+    $atom:a19  $mol   @atom:B    0.0   -0.57472665 -0.82852797 -0.27027791
+    $atom:a20  $mol   @atom:L    0.0   -1.3967448 -1.0516787 0.24247346
+    $atom:a21  $mol   @atom:L    0.0   -1.003428 -0.85642681 1.1107555
+    $atom:a22  $mol   @atom:B    0.0   -0.25156735 -0.3182346 0.74262946
+    $atom:a23  $mol   @atom:B    0.0   -0.61751956 0.30115562 0.070426493
+    $atom:a24  $mol   @atom:L    0.0   -1.3347934 0.83310182 0.52625934
+    $atom:a25  $mol   @atom:L    0.0   -0.83315257 1.270904 1.2564086
+    $atom:a26  $mol   @atom:B    0.0   -0.10469759 1.6988523 0.72597181
+    $atom:a27  $mol   @atom:L    0.0   -0.57854905 2.3367737 0.11206868
+  }
+
+} # 1beadMisfolded
+
+
+1beadUnfolded inherits 1beadFrustrated {
+
+  # This molecule "inherits" all of its features from "1beadFrustrated"
+  # Here we override the atomic positions with new coordinates:
+
+  #  AtomID MoleculeID AtomType Charge   X        Y         Z
+
+  write('Data Atoms') {
+    $atom:a1   $mol   @atom:L    0.0    -2.4      1.7      -0.0
+    $atom:a2   $mol   @atom:B    0.0    -1.8      1.7       0.8
+    $atom:a3   $mol   @atom:L    0.0    -1.2      2.5       0.8
+    $atom:a4   $mol   @atom:B    0.0    -0.6      2.5      -0.0
+    $atom:a5   $mol   @atom:L    0.0     0.0      1.7      -0.0
+    $atom:a6   $mol   @atom:B    0.0     0.6      1.7       0.8
+    $atom:a7   $mol   @atom:N    0.0     1.2      2.5       0.8
+    $atom:a8   $mol   @atom:N    0.0     1.8      2.5      -0.0
+    $atom:a9   $mol   @atom:B    0.0     2.4      1.7      -0.0
+    $atom:a10  $mol   @atom:L    0.0     3.0      1.7      -0.8
+    $atom:a11  $mol   @atom:B    0.0     3.0      0.7      -0.8
+    $atom:a12  $mol   @atom:L    0.0     3.0      0.1      -0.0
+    $atom:a13  $mol   @atom:B    0.0     3.8     -0.5      -0.0
+    $atom:a14  $mol   @atom:L    0.0     3.8     -1.1      -0.8
+    $atom:a15  $mol   @atom:N    0.0     3.0     -1.7      -0.8
+    $atom:a16  $mol   @atom:N    0.0     3.0     -1.7       0.2
+    $atom:a17  $mol   @atom:N    0.0     2.4     -2.5       0.2
+    $atom:a18  $mol   @atom:B    0.0     1.8     -2.5      -0.6
+    $atom:a19  $mol   @atom:B    0.0     1.2     -1.7      -0.6
+    $atom:a20  $mol   @atom:L    0.0     0.6     -1.7       0.2
+    $atom:a21  $mol   @atom:L    0.0    -0.0     -2.5       0.2
+    $atom:a22  $mol   @atom:B    0.0    -0.6     -2.5      -0.6
+    $atom:a23  $mol   @atom:B    0.0    -1.2     -1.7      -0.6
+    $atom:a24  $mol   @atom:L    0.0    -1.8     -1.7       0.2
+    $atom:a25  $mol   @atom:L    0.0    -2.4     -2.5       0.2
+    $atom:a26  $mol   @atom:B    0.0    -3.0     -2.5      -0.6
+    $atom:a27  $mol   @atom:L    0.0    -3.6     -1.7      -0.6
+  }
+
+} # 1beadUnfolded
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py

@@ -0,0 +1,67 @@
+#!/usr/bin/env python
+
+# Calculate a table of dihedral angle interactions used in the alpha-helix
+# and beta-sheet regions of the frustrated protein model described in
+#  provided in figure 8 of the supplemental materials section of:
+# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
+# Note that the "A" and "B" parameters were incorrectly reported to be 
+# 5.4*epsilon and 6.0*epsilon.  The values used were 5.6 and 6.0 epsilon.
+# The phiA and phiB values were 57.29577951308232 degrees (1 rad) 
+# and 180 degrees, respectively.  Both expA and expB were 6.0.
+#
+# To generate the table used for the alpha-helix (1 degree resolution) use this:
+#  ./calc_dihedral_table.py 6.0 57.29577951308232 6  5.6 180 6  0.0 359  360
+# To generate the table used for the beta-sheets (1 degree resolution) use this:
+#  ./calc_dihedral_table.py 5.6 57.29577951308232 6  6.0 180 6  0.0 359  360
+#
+# (If you're curious as to why I set the location of the minima at phi_alpha
+#  to 1.0 radians (57.2957795 degrees), there was no particularly good reason.
+#  I think the correct value turns out to be something closer to 50 degrees.)
+
+
+from math import *
+import sys
+
+
+# The previous version included the repulsive core term
+def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
+    conv_units = pi/180.0
+    if use_radians:
+        conv_units = 1.0
+    termA = pow(cos(0.5*(phi-phiA)*conv_units), expA)
+    termB = pow(cos(0.5*(phi-phiB)*conv_units), expB)
+    return -A*termA - B*termB
+
+# The previous version included the repulsive core term
+def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
+    conv_units = pi/180.0
+    if use_radians:
+        conv_units = 1.0
+    termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * 
+             expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0))
+    termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * 
+             expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0))
+    return -conv_units*(A*termA + B*termB)
+
+if len(sys.argv) != 10:
+    sys.stderr.write("Error: expected 9 arguments:\n"
+                     "\n"
+                     "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n")
+    sys.exit(-1)
+
+A       = float(sys.argv[1])
+phiA    = float(sys.argv[2])
+expA    = float(sys.argv[3])
+B       = float(sys.argv[4])
+phiB    = float(sys.argv[5])
+expB    = float(sys.argv[6])
+phi_min = float(sys.argv[7])
+phi_max = float(sys.argv[8])
+N       =   int(sys.argv[9])
+
+for i in range(0,N):
+    phi = phi_min + i*(phi_max - phi_min)/(N-1)
+    U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
+    F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
+    print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi))
+

tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt

@@ -0,0 +1,20 @@
+import "1beadFrustrated_variants.lt"
+
+
+protein  =  new 1beadUnfolded
+
+
+
+# Note: The protein begins in an "Unfolded" conformation.  If instead
+#       you want it to begin in the folded or misfolded conformations use:
+# protein  =  new 1beadFrustrated   # or
+# protein  =  new 1beadMisfolded
+
+
+
+# ("27.0" is the length of the protein when maximally extended)
+write_once("Data Boundary") {
+  0.0  27.0  xlo xhi
+  0.0  27.0  ylo yhi
+  0.0  27.0  zlo zhi
+}