Merge pull request #640 from ohenrich/user-cgdna

USER-CGDNA - sequence-dependent stacking and h-bonding strength

doc/src/fix_nve_dot.txt

@@ -44,7 +44,7 @@ A technical report with more information on this integrator can be found
 [Restrictions:]
 
 These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
+"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/fix_nve_dotc_langevin.txt

@@ -24,7 +24,8 @@ keyword = {angmom} :l
 
 [Examples:]
 
-fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre
+fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 
+fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10 :pre
 
 [Description:]
 
@@ -78,7 +79,9 @@ a Gaussian random number) for speed.
 :line
 
 {Tstart} and {Tstop} have to be constant values, i.e. they cannot
-be variables.
+be variables. If used together with the oxDNA force field for 
+coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units
+corresponds to T = 300 K.  
 
 The {damp} parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 0.03
@@ -89,6 +92,10 @@ viscosity of the solvent, i.e. a small relaxation time implies a
 hi-viscosity solvent and vice versa.  See the discussion about gamma
 and viscosity in the documentation for the "fix
 viscous"_fix_viscous.html command for more details.
+Note that the value 78.9375 in the second example above corresponds 
+to a diffusion constant, which is about an order of magnitude larger 
+than realistic ones. This has been used to sample configurations faster
+in Brownian dynamics simulations. 
 
 The random # {seed} must be a positive integer. A Marsaglia random
 number generator is used.  Each processor uses the input seed to
@@ -115,12 +122,12 @@ A technical report with more information on this integrator can be found
 [Restrictions:]
 
 These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
+"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]
 
-"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,
+"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, "bond_style oxdna/fene"_bond_oxdna.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
 
 [Default:] none
 

doc/src/pair_oxdna.txt

@@ -20,20 +20,24 @@ pair_coeff * * style2 args :pre
 
 style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul
 
-style2 = {oxdna/stk}
+style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
-args = list of arguments for these two particular styles :ul
+args = list of arguments for these particular styles :ul
 
-  {oxdna2/stk} args = T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+  {oxdna/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-    T = temperature (oxDNA units, 0.1 = 300 K) :pre
+    seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
+    T = temperature (oxDNA units, 0.1 = 300 K) 
+  {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+    seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
+    eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre 
 
 [Examples:]
 
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/stk     seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
 
@@ -44,10 +48,11 @@ for coarse-grained modelling of DNA. The effective interaction between the nucle
 excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
 and coaxial stacking interaction {oxdna/coaxstk} as well
 as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
-opposite strands.
+opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
+are supported "(Sulc)"_#Sulc1.
 
-The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients
+The exact functional form of the pair styles is rather complex.
-in the above example. The individual potentials consist of products of modulation factors,
+The individual potentials consist of products of modulation factors,
 which themselves are constructed from a number of more basic potentials
 (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
 We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1
@@ -55,9 +60,10 @@ for a detailed description of the oxDNA force field.
 
 NOTE: These pair styles have to be used together with the related oxDNA bond style
 {oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna/fene"_bond_oxdna.html). With one exception the coefficients
+"bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients
 in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example).
+Exceptions are the first and second coefficient after {oxdna/stk} (seq=seqdep and T=0.1 in the above example)
+and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example).
 When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
 or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
 the temperature coefficients have to be matched to the one used in the fix.
@@ -86,7 +92,11 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 :line
 
+:link(Sulc1)
+[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
 :link(Ouldridge-DPhil1)
 [(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+
 :link(Ouldridge1)
 [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).

doc/src/pair_oxdna2.txt

@@ -21,11 +21,15 @@ pair_coeff * * style2 args :pre
 
 style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh} :ul
 
-style2 = {oxdna2/stk} or {oxdna2/dh}
+style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
-args = list of arguments for these two particular styles :ul
+args = list of arguments for these particular styles :ul
 
-  {oxdna2/stk} args = T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+  {oxdna2/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+    seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
     T = temperature (oxDNA units, 0.1 = 300 K)
+  {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+    seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
+    eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
   {oxdna2/dh} args = T rhos qeff
     T = temperature (oxDNA units, 0.1 = 300 K)
     rhos = salt concentration (mole per litre)
@@ -35,10 +39,10 @@ args = list of arguments for these two particular styles :ul
 
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815 :pre
@@ -50,7 +54,8 @@ for coarse-grained modelling of DNA. The effective interaction between the nucle
 excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk}
 and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
 as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
-opposite strands.
+opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
+are supported "(Sulc)"_#Sulc2.
 
 The exact functional form of the pair styles is rather complex.
 The individual potentials consist of products of modulation factors,
@@ -61,9 +66,10 @@ and  "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force fi
 
 NOTE: These pair styles have to be used together with the related oxDNA2 bond style
 {oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna2/fene"_bond_oxdna.html). Almost all coefficients
+"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients
 in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients
+Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example),
+the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients 
 after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
 e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
 the temperature coefficients have to be matched to the one used in the fix.
@@ -92,6 +98,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 :line
 
+:link(Sulc2)
+[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
 :link(Snodin)
 [(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
 

examples/USER/cgdna/examples/oxDNA/duplex1/input.duplex1

@@ -30,10 +30,10 @@ bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 

examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.1

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 

examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.4

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 

examples/USER/cgdna/examples/oxDNA/duplex2/input.duplex2

@@ -30,10 +30,10 @@ bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 

examples/USER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.1

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 

examples/USER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.4

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 

examples/USER/cgdna/examples/oxDNA2/duplex1/input.duplex1

@@ -30,10 +30,10 @@ bond_coeff * 2.0 0.25 0.7564
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815

examples/USER/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.1

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7564
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815

examples/USER/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.4

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7564
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815

examples/USER/cgdna/examples/oxDNA2/duplex2/input.duplex2

@@ -30,10 +30,10 @@ bond_coeff * 2.0 0.25 0.7564
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815

examples/USER/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.1

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7564
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815

examples/USER/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.4

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7564
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815

src/USER-CGDNA/pair_oxdna_hbond.cpp

@@ -38,6 +38,14 @@ using namespace LAMMPS_NS;
 using namespace MathConst;
 using namespace MFOxdna;
 
+// sequence-specific base-pairing strength
+// A:0 C:1 G:2 T:3, 5'- (i,j) -3'
+static const double alpha[4][4] = 
+{{1.00000,1.00000,1.00000,0.82915},
+ {1.00000,1.00000,1.15413,1.00000},
+ {1.00000,1.15413,1.00000,1.00000},
+ {0.82915,1.00000,1.00000,1.00000}};
+
 /* ---------------------------------------------------------------------- */
 
 PairOxdnaHbond::PairOxdnaHbond(LAMMPS *lmp) : Pair(lmp)
@@ -607,7 +615,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
 {
   int count;
 
-  if (narg != 26) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/hbond");
+  if (narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/hbond");
   if (!allocated) allocate();
 
   int ilo,ihi,jlo,jhi;
@@ -638,36 +646,42 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
   double a_hb8_one, theta_hb8_0_one, dtheta_hb8_ast_one;
   double b_hb8_one, dtheta_hb8_c_one;
 
-  epsilon_hb_one = force->numeric(FLERR,arg[2]);
+  if (strcmp(arg[2], "seqav") != 0 && strcmp(arg[2], "seqdep") != 0) {
-  a_hb_one = force->numeric(FLERR,arg[3]);
+    error->all(FLERR,"Incorrect setting, select seqav or seqdep in oxdna/hbond");
-  cut_hb_0_one = force->numeric(FLERR,arg[4]);
+  }
-  cut_hb_c_one = force->numeric(FLERR,arg[5]);
+  if (strcmp(arg[2],"seqav")  == 0) seqdepflag = 0;
-  cut_hb_lo_one = force->numeric(FLERR,arg[6]);
+  if (strcmp(arg[2],"seqdep") == 0) seqdepflag = 1;
-  cut_hb_hi_one = force->numeric(FLERR,arg[7]);
 
-  a_hb1_one = force->numeric(FLERR,arg[8]);
+  epsilon_hb_one = force->numeric(FLERR,arg[3]);
-  theta_hb1_0_one = force->numeric(FLERR,arg[9]);
+  a_hb_one = force->numeric(FLERR,arg[4]);
-  dtheta_hb1_ast_one = force->numeric(FLERR,arg[10]);
+  cut_hb_0_one = force->numeric(FLERR,arg[5]);
+  cut_hb_c_one = force->numeric(FLERR,arg[6]);
+  cut_hb_lo_one = force->numeric(FLERR,arg[7]);
+  cut_hb_hi_one = force->numeric(FLERR,arg[8]);
 
-  a_hb2_one = force->numeric(FLERR,arg[11]);
+  a_hb1_one = force->numeric(FLERR,arg[9]);
-  theta_hb2_0_one = force->numeric(FLERR,arg[12]);
+  theta_hb1_0_one = force->numeric(FLERR,arg[10]);
-  dtheta_hb2_ast_one = force->numeric(FLERR,arg[13]);
+  dtheta_hb1_ast_one = force->numeric(FLERR,arg[11]);
 
-  a_hb3_one = force->numeric(FLERR,arg[14]);
+  a_hb2_one = force->numeric(FLERR,arg[12]);
-  theta_hb3_0_one = force->numeric(FLERR,arg[15]);
+  theta_hb2_0_one = force->numeric(FLERR,arg[13]);
-  dtheta_hb3_ast_one = force->numeric(FLERR,arg[16]);
+  dtheta_hb2_ast_one = force->numeric(FLERR,arg[14]);
 
-  a_hb4_one = force->numeric(FLERR,arg[17]);
+  a_hb3_one = force->numeric(FLERR,arg[15]);
-  theta_hb4_0_one = force->numeric(FLERR,arg[18]);
+  theta_hb3_0_one = force->numeric(FLERR,arg[16]);
-  dtheta_hb4_ast_one = force->numeric(FLERR,arg[19]);
+  dtheta_hb3_ast_one = force->numeric(FLERR,arg[17]);
 
-  a_hb7_one = force->numeric(FLERR,arg[20]);
+  a_hb4_one = force->numeric(FLERR,arg[18]);
-  theta_hb7_0_one = force->numeric(FLERR,arg[21]);
+  theta_hb4_0_one = force->numeric(FLERR,arg[19]);
-  dtheta_hb7_ast_one = force->numeric(FLERR,arg[22]);
+  dtheta_hb4_ast_one = force->numeric(FLERR,arg[20]);
 
-  a_hb8_one = force->numeric(FLERR,arg[23]);
+  a_hb7_one = force->numeric(FLERR,arg[21]);
-  theta_hb8_0_one = force->numeric(FLERR,arg[24]);
+  theta_hb7_0_one = force->numeric(FLERR,arg[22]);
-  dtheta_hb8_ast_one = force->numeric(FLERR,arg[25]);
+  dtheta_hb7_ast_one = force->numeric(FLERR,arg[23]);
+
+  a_hb8_one = force->numeric(FLERR,arg[24]);
+  theta_hb8_0_one = force->numeric(FLERR,arg[25]);
+  dtheta_hb8_ast_one = force->numeric(FLERR,arg[26]);
 
   b_hb_lo_one = 2*a_hb_one*exp(-a_hb_one*(cut_hb_lo_one-cut_hb_0_one))*
         2*a_hb_one*exp(-a_hb_one*(cut_hb_lo_one-cut_hb_0_one))*
@@ -718,6 +732,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
     for (int j = MAX(jlo,i); j <= jhi; j++) {
 
       epsilon_hb[i][j] = epsilon_hb_one;
+      if (seqdepflag) epsilon_hb[i][j] *= alpha[i-1][j-1];
       a_hb[i][j] = a_hb_one;
       cut_hb_0[i][j] = cut_hb_0_one;
       cut_hb_c[i][j] = cut_hb_c_one;
@@ -728,6 +743,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
       b_hb_lo[i][j] = b_hb_lo_one;
       b_hb_hi[i][j] = b_hb_hi_one;
       shift_hb[i][j] = shift_hb_one;
+      if (seqdepflag) shift_hb[i][j] *= alpha[i-1][j-1];
 
       a_hb1[i][j] = a_hb1_one;
       theta_hb1_0[i][j] = theta_hb1_0_one;
@@ -814,7 +830,12 @@ double PairOxdnaHbond::init_one(int i, int j)
     error->all(FLERR,"Offset not supported in oxDNA");
   }
 
-  epsilon_hb[j][i] = epsilon_hb[i][j];
+  if (seqdepflag) {
+    epsilon_hb[j][i] = epsilon_hb[i][j] / alpha[i-1][j-1] * alpha[j-1][i-1];
+  }
+  else {
+    epsilon_hb[j][i] = epsilon_hb[i][j];
+  }
   a_hb[j][i] = a_hb[i][j];
   cut_hb_0[j][i] = cut_hb_0[i][j];
   cut_hb_c[j][i] = cut_hb_c[i][j];
@@ -824,7 +845,12 @@ double PairOxdnaHbond::init_one(int i, int j)
   b_hb_hi[j][i] = b_hb_hi[i][j];
   cut_hb_lc[j][i] = cut_hb_lc[i][j];
   cut_hb_hc[j][i] = cut_hb_hc[i][j];
-  shift_hb[j][i] = shift_hb[i][j];
+  if (seqdepflag) {
+    shift_hb[j][i] = shift_hb[i][j] / alpha[i-1][j-1] * alpha[j-1][i-1];
+  }
+  else {
+    shift_hb[j][i] = shift_hb[i][j];
+  }
 
   a_hb1[j][i] = a_hb1[i][j];
   theta_hb1_0[j][i] = theta_hb1_0[i][j];

src/USER-CGDNA/pair_oxdna_hbond.h

@@ -67,6 +67,8 @@ class PairOxdnaHbond : public Pair {
   double **a_hb8, **theta_hb8_0, **dtheta_hb8_ast;
   double **b_hb8, **dtheta_hb8_c;
 
+  int seqdepflag;
+
   virtual void allocate();
 };
 

src/USER-CGDNA/pair_oxdna_stk.cpp

@@ -38,6 +38,14 @@ using namespace LAMMPS_NS;
 using namespace MathConst;
 using namespace MFOxdna;
 
+// sequence-specific stacking strength
+// A:0 C:1 G:2 T:3, 5'- (i,j) -3'
+static const double alpha[4][4] =
+{{1.11960,1.00852,0.96950,0.99632},
+ {1.01889,0.97804,1.02681,0.96950},
+ {0.98169,1.05913,0.97804,1.00852},
+ {0.94694,0.98169,1.01889,0.96383}};
+
 /* ---------------------------------------------------------------------- */
 
 PairOxdnaStk::PairOxdnaStk(LAMMPS *lmp) : Pair(lmp)
@@ -194,6 +202,7 @@ void PairOxdnaStk::compute(int eflag, int vflag)
 
     }
 
+    // a now in 5' direction, b in 3' direction
     atype = type[a];
     btype = type[b];
 
@@ -665,7 +674,7 @@ void PairOxdnaStk::coeff(int narg, char **arg)
 {
   int count;
 
-  if (narg != 21) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk");
+  if (narg != 22) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk");
   if (!allocated) allocate();
 
   int ilo,ihi,jlo,jhi;
@@ -691,28 +700,34 @@ void PairOxdnaStk::coeff(int narg, char **arg)
   double a_st1_one, cosphi_st1_ast_one, b_st1_one, cosphi_st1_c_one;
   double a_st2_one, cosphi_st2_ast_one, b_st2_one, cosphi_st2_c_one;
 
-  T = force->numeric(FLERR,arg[2]);
+  if (strcmp(arg[2], "seqav") != 0 && strcmp(arg[2], "seqdep") != 0) {
+    error->all(FLERR,"Incorrect setting, select seqav or seqdep in oxdna/stk");
+  }
+  if (strcmp(arg[2],"seqav")  == 0) seqdepflag = 0;
+  if (strcmp(arg[2],"seqdep") == 0) seqdepflag = 1;
+
+  T = force->numeric(FLERR,arg[3]);
   epsilon_st_one = stacking_strength(T);
 
-  a_st_one = force->numeric(FLERR,arg[3]);
+  a_st_one = force->numeric(FLERR,arg[4]);
-  cut_st_0_one = force->numeric(FLERR,arg[4]);
+  cut_st_0_one = force->numeric(FLERR,arg[5]);
-  cut_st_c_one = force->numeric(FLERR,arg[5]);
+  cut_st_c_one = force->numeric(FLERR,arg[6]);
-  cut_st_lo_one = force->numeric(FLERR,arg[6]);
+  cut_st_lo_one = force->numeric(FLERR,arg[7]);
-  cut_st_hi_one = force->numeric(FLERR,arg[7]);
+  cut_st_hi_one = force->numeric(FLERR,arg[8]);
 
-  a_st4_one = force->numeric(FLERR,arg[8]);
+  a_st4_one = force->numeric(FLERR,arg[9]);
-  theta_st4_0_one = force->numeric(FLERR,arg[9]);
+  theta_st4_0_one = force->numeric(FLERR,arg[10]);
-  dtheta_st4_ast_one = force->numeric(FLERR,arg[10]);
+  dtheta_st4_ast_one = force->numeric(FLERR,arg[11]);
-  a_st5_one = force->numeric(FLERR,arg[11]);
+  a_st5_one = force->numeric(FLERR,arg[12]);
-  theta_st5_0_one = force->numeric(FLERR,arg[12]);
+  theta_st5_0_one = force->numeric(FLERR,arg[13]);
-  dtheta_st5_ast_one = force->numeric(FLERR,arg[13]);
+  dtheta_st5_ast_one = force->numeric(FLERR,arg[14]);
-  a_st6_one = force->numeric(FLERR,arg[14]);
+  a_st6_one = force->numeric(FLERR,arg[15]);
-  theta_st6_0_one = force->numeric(FLERR,arg[15]);
+  theta_st6_0_one = force->numeric(FLERR,arg[16]);
-  dtheta_st6_ast_one = force->numeric(FLERR,arg[16]);
+  dtheta_st6_ast_one = force->numeric(FLERR,arg[17]);
-  a_st1_one = force->numeric(FLERR,arg[17]);
+  a_st1_one = force->numeric(FLERR,arg[18]);
-  cosphi_st1_ast_one = force->numeric(FLERR,arg[18]);
+  cosphi_st1_ast_one = force->numeric(FLERR,arg[19]);
-  a_st2_one = force->numeric(FLERR,arg[19]);
+  a_st2_one = force->numeric(FLERR,arg[20]);
-  cosphi_st2_ast_one = force->numeric(FLERR,arg[20]);
+  cosphi_st2_ast_one = force->numeric(FLERR,arg[21]);
 
   b_st_lo_one = 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))*
         2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))*
@@ -756,11 +771,11 @@ void PairOxdnaStk::coeff(int narg, char **arg)
   b_st2_one = a_st2_one*a_st2_one*cosphi_st2_ast_one*cosphi_st2_ast_one/(1-a_st2_one*cosphi_st2_ast_one*cosphi_st2_ast_one);
   cosphi_st2_c_one=1/(a_st2_one*cosphi_st2_ast_one);
 
-
   for (int i = ilo; i <= ihi; i++) {
     for (int j = MAX(jlo,i); j <= jhi; j++) {
 
       epsilon_st[i][j] = epsilon_st_one;
+      if (seqdepflag) epsilon_st[i][j] *= alpha[i-1][j-1];
       a_st[i][j] = a_st_one;
       cut_st_0[i][j] = cut_st_0_one;
       cut_st_c[i][j] = cut_st_c_one;
@@ -771,6 +786,7 @@ void PairOxdnaStk::coeff(int narg, char **arg)
       b_st_lo[i][j] = b_st_lo_one;
       b_st_hi[i][j] = b_st_hi_one;
       shift_st[i][j] = shift_st_one;
+      if (seqdepflag) shift_st[i][j] *= alpha[i-1][j-1];
 
       a_st4[i][j] = a_st4_one;
       theta_st4_0[i][j] = theta_st4_0_one;
@@ -849,7 +865,12 @@ double PairOxdnaStk::init_one(int i, int j)
     error->all(FLERR,"Offset not supported in oxDNA");
   }
 
-  epsilon_st[j][i] = epsilon_st[i][j];
+  if (seqdepflag) {
+    epsilon_st[j][i] = epsilon_st[i][j]  / alpha[i-1][j-1] * alpha[j-1][i-1];
+  }
+  else {
+    epsilon_st[j][i] = epsilon_st[i][j];
+  }
   a_st[j][i] = a_st[i][j];
   b_st_lo[j][i] = b_st_lo[i][j];
   b_st_hi[j][i] = b_st_hi[i][j];
@@ -859,7 +880,12 @@ double PairOxdnaStk::init_one(int i, int j)
   cut_st_hi[j][i] = cut_st_hi[i][j];
   cut_st_lc[j][i] = cut_st_lc[i][j];
   cut_st_hc[j][i] = cut_st_hc[i][j];
-  shift_st[j][i] = shift_st[i][j];
+  if (seqdepflag) {
+    shift_st[j][i] = shift_st[i][j] / alpha[i-1][j-1] * alpha[j-1][i-1];
+  }
+  else {
+    shift_st[j][i] = shift_st[i][j];
+  }
 
   a_st4[j][i] = a_st4[i][j];
   theta_st4_0[j][i] = theta_st4_0[i][j];

src/USER-CGDNA/pair_oxdna_stk.h

@@ -58,6 +58,8 @@ class PairOxdnaStk : public Pair {
   double **a_st1, **cosphi_st1_ast, **b_st1, **cosphi_st1_c;
   double **a_st2, **cosphi_st2_ast, **b_st2, **cosphi_st2_c;
 
+  int seqdepflag;
+
   virtual void allocate();
 };