Merge pull request #440 from ohenrich/user-cgdna

Updated lammps.book, USER-CGDNA install script

doc/src/lammps.book

@@ -464,6 +464,7 @@ pair_nb3b_harmonic.html
 pair_nm.html
 pair_none.html
 pair_oxdna.html
+pair_oxdna2.html
 pair_peri.html
 pair_polymorphic.html
 pair_quip.html

src/USER-CGDNA/Install.sh

@@ -29,19 +29,29 @@ action () {
 # list of files with dependcies
 
 action  bond_oxdna_fene.cpp bond_fene.h
+action  bond_oxdna2_fene.cpp bond_fene.h
 action  bond_oxdna_fene.h bond_fene.h
+action  bond_oxdna2_fene.h bond_fene.h
 action  fix_nve_dotc_langevin.cpp atom_vec_ellipsoid.h
 action  fix_nve_dotc_langevin.h atom_vec_ellipsoid.h
 action  fix_nve_dot.cpp atom_vec_ellipsoid.h
 action  fix_nve_dot.h atom_vec_ellipsoid.h
 action  mf_oxdna.h atom_vec_ellipsoid.h
 action  pair_oxdna_coaxstk.cpp atom_vec_ellipsoid.h
+action  pair_oxdna2_coaxstk.cpp atom_vec_ellipsoid.h
 action  pair_oxdna_coaxstk.h atom_vec_ellipsoid.h
+action  pair_oxdna2_coaxstk.h atom_vec_ellipsoid.h
 action  pair_oxdna_excv.cpp atom_vec_ellipsoid.h
+action  pair_oxdna2_excv.cpp atom_vec_ellipsoid.h
 action  pair_oxdna_excv.h atom_vec_ellipsoid.h
+action  pair_oxdna2_excv.h atom_vec_ellipsoid.h
 action  pair_oxdna_hbond.cpp atom_vec_ellipsoid.h
 action  pair_oxdna_hbond.h atom_vec_ellipsoid.h
 action  pair_oxdna_stk.cpp atom_vec_ellipsoid.h
+action  pair_oxdna2_stk.cpp atom_vec_ellipsoid.h
 action  pair_oxdna_stk.h atom_vec_ellipsoid.h
+action  pair_oxdna2_stk.h atom_vec_ellipsoid.h
 action  pair_oxdna_xstk.cpp atom_vec_ellipsoid.h
 action  pair_oxdna_xstk.h atom_vec_ellipsoid.h
+action  pair_oxdna2_dh.cpp atom_vec_ellipsoid.h
+action  pair_oxdna2_dh.h atom_vec_ellipsoid.h

src/USER-CGDNA/README

@@ -2,9 +2,9 @@ This package contains a LAMMPS implementation of coarse-grained
 models of DNA, which can be used to model sequence-specific
 DNA strands.
 
-See the doc pages and [1,2] for the individual bond and pair styles. 
+See the doc pages and [1,2,3] for the individual bond and pair styles. 
 The packages contains also a new Langevin-type rigid-body integrator,
-which has also its own doc page and is explained in [3].
+which has also its own doc page and is explained in [4].
 
 [1] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical, 
 and thermodynamic properties of a coarse-grained DNA model",
@@ -13,16 +13,20 @@ J. Chem. Phys. 134, 085101 (2011).
 [2] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA 
 self-assembly, DPhil. University of Oxford (2011).
 
-[3] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and 
+[3] B.E. Snodin, F. Randisi, M. Mosayebi, et al., Introducing
+Improved Structural Properties and Salt Dependence into a Coarse-Grained
+Model of DNA, J. Chem. Phys. 142, 234901 (2015).
+
+[4] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and 
 gradient thermostats for rigid body dynamics", J. Chem. Phys. 142, 
 144114 (2015).
 
 Example input and data files can be found in
-/examples/USER/cgdna/examples/duplex1/ and /duplex2/.  A simple python
-setup tool which creates single straight or helical DNA strands as
-well as DNA duplexes and arrays of duplexes can be found in
-/examples/USER/cgdna/util/.  A technical report with more information
-on the model, the structure of the input and data file, the setup tool
+/examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. Python setup 
+tools which create single straight or helical DNA strands as
+well as DNA duplexes or arrays of duplexes can be found in
+/examples/USER/cgdna/util/. A technical report with more information
+on the models, the structure of the input and data file, the setup tool
 and the performance of the LAMMPS-implementation of oxDNA can be found
 in /doc/src/PDF/USER-CGDNA-overview.pdf.
 
@@ -35,6 +39,7 @@ of the LAMMPS manual).
 The creator of this package is:
 
 Dr Oliver Henrich
+University of Strathclyde, UK
 University of Edinburgh, UK
 ohenrich@ph.ed.ac.uk
 o.henrich@epcc.ed.ac.uk
@@ -45,6 +50,8 @@ o.henrich@epcc.ed.ac.uk
 
 bond_oxdna_fene.cpp:  backbone connectivity, a modified FENE potential
 
+bond_oxdna2_fene.cpp: corresponding bond style in oxDNA2 (see [3])
+
 ** Pair styles provided by this package:
 
 pair_oxdna_excv.cpp:  excluded volume interaction between the nucleotides
@@ -59,6 +66,13 @@ pair_oxdna_xstk.cpp:  cross-stacking interaction between nucleotides
 
 pair_oxdna_coaxstk.cpp:  coaxial stacking interaction between nucleotides
 
+
+pair_oxdna2_excv.cpp, pair_oxdna2_stk.cpp, pair_oxdna2_coaxstk.cpp:
+		     corresponding pair styles in oxDNA2 (see [3])
+
+pair_oxdna2_dh.cpp:  Debye-Hueckel electrostatic interaction between backbone
+		     sites
+
 ** Fixes provided by this package:
 
 fix_nve_dotc_langevin.cpp:  fix for Langevin-type rigid body integrator "C"