forked from lijiext/lammps
Merge pull request #640 from ohenrich/user-cgdna
USER-CGDNA - sequence-dependent stacking and h-bonding strength
This commit is contained in:
Steve Plimpton
GitHub
commit
4161868bcf
Binary file not shown.
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@ -44,7 +44,7 @@ A technical report with more information on this integrator can be found
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[Restrictions:]
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These pair styles can only be used if LAMMPS was built with the
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USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
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"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info on packages.
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[Related commands:]
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@ -24,7 +24,8 @@ keyword = {angmom} :l
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[Examples:]
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fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre
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fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10
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fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10 :pre
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[Description:]
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@ -78,7 +79,9 @@ a Gaussian random number) for speed.
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:line
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{Tstart} and {Tstop} have to be constant values, i.e. they cannot
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be variables.
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be variables. If used together with the oxDNA force field for
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coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units
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corresponds to T = 300 K.
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The {damp} parameter is specified in time units and determines how
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rapidly the temperature is relaxed. For example, a value of 0.03
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@ -89,6 +92,10 @@ viscosity of the solvent, i.e. a small relaxation time implies a
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hi-viscosity solvent and vice versa. See the discussion about gamma
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and viscosity in the documentation for the "fix
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viscous"_fix_viscous.html command for more details.
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Note that the value 78.9375 in the second example above corresponds
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to a diffusion constant, which is about an order of magnitude larger
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than realistic ones. This has been used to sample configurations faster
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in Brownian dynamics simulations.
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The random # {seed} must be a positive integer. A Marsaglia random
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number generator is used. Each processor uses the input seed to
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@ -115,12 +122,12 @@ A technical report with more information on this integrator can be found
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[Restrictions:]
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These pair styles can only be used if LAMMPS was built with the
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USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
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"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info on packages.
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[Related commands:]
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"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,
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"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
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[Default:] none
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@ -20,20 +20,24 @@ pair_coeff * * style2 args :pre
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style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul
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style2 = {oxdna/stk}
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args = list of arguments for these two particular styles :ul
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style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
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args = list of arguments for these particular styles :ul
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{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
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T = temperature (oxDNA units, 0.1 = 300 K) :pre
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{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
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seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
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T = temperature (oxDNA units, 0.1 = 300 K)
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{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
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seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
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eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre
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[Examples:]
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pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
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pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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@ -44,10 +48,11 @@ for coarse-grained modelling of DNA. The effective interaction between the nucle
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excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
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and coaxial stacking interaction {oxdna/coaxstk} as well
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as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
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opposite strands.
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opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
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are supported "(Sulc)"_#Sulc1.
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The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients
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in the above example. The individual potentials consist of products of modulation factors,
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The exact functional form of the pair styles is rather complex.
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The individual potentials consist of products of modulation factors,
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which themselves are constructed from a number of more basic potentials
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(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
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We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1
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@ -55,9 +60,10 @@ for a detailed description of the oxDNA force field.
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NOTE: These pair styles have to be used together with the related oxDNA bond style
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{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
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"bond_style oxdna/fene"_bond_oxdna.html). With one exception the coefficients
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"bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients
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in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
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The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example).
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Exceptions are the first and second coefficient after {oxdna/stk} (seq=seqdep and T=0.1 in the above example)
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and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example).
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When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
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or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
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the temperature coefficients have to be matched to the one used in the fix.
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@ -86,7 +92,11 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
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:line
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:link(Sulc1)
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[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
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:link(Ouldridge-DPhil1)
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[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
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:link(Ouldridge1)
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[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
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@ -21,11 +21,15 @@ pair_coeff * * style2 args :pre
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style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh} :ul
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style2 = {oxdna2/stk} or {oxdna2/dh}
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args = list of arguments for these two particular styles :ul
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style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
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args = list of arguments for these particular styles :ul
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{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
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{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
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seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
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T = temperature (oxDNA units, 0.1 = 300 K)
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{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
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seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
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eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
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{oxdna2/dh} args = T rhos qeff
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T = temperature (oxDNA units, 0.1 = 300 K)
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rhos = salt concentration (mole per litre)
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@ -35,10 +39,10 @@ args = list of arguments for these two particular styles :ul
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pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
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pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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pair_coeff * * oxdna2/dh 0.1 1.0 0.815 :pre
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@ -50,7 +54,8 @@ for coarse-grained modelling of DNA. The effective interaction between the nucle
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excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk}
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and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
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as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
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opposite strands.
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opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
|
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are supported "(Sulc)"_#Sulc2.
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The exact functional form of the pair styles is rather complex.
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The individual potentials consist of products of modulation factors,
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@ -61,9 +66,10 @@ and "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force fi
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NOTE: These pair styles have to be used together with the related oxDNA2 bond style
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{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
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"bond_style oxdna2/fene"_bond_oxdna.html). Almost all coefficients
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"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients
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in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
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Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients
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Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example),
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the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients
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after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
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e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
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the temperature coefficients have to be matched to the one used in the fix.
|
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|
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@ -92,6 +98,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
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|
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:line
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:link(Sulc2)
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[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
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:link(Snodin)
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[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
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@ -30,10 +30,10 @@ bond_coeff * 2.0 0.25 0.7525
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# oxDNA pair interactions
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pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
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pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7525
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# 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/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 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 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 * * 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 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 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 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
|
||||
|
||||
|
|
|
|||
|
|
@ -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/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 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 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 * * 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 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 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 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
|
||||
|
||||
|
|
|
|||
|
|
@ -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/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 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 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 * * 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 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 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 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
|
||||
|
||||
|
|
|
|||
|
|
@ -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/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 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 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 * * 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 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 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 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
|
||||
|
||||
|
|
|
|||
|
|
@ -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/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 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 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 * * 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 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 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 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
|
||||
|
||||
|
|
|
|||
|
|
@ -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/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 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 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 * * 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 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 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 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
|
||||
|
|
|
|||
|
|
@ -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/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 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 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 * * 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 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 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 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
|
||||
|
|
|
|||
|
|
@ -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/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 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 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 * * 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 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 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 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
|
||||
|
|
|
|||
|
|
@ -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/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 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 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 * * 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 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 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 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
|
||||
|
|
|
|||
|
|
@ -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/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 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 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 * * 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 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 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 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
|
||||
|
|
|
|||
|
|
@ -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/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 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 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 * * 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 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 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 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
|
||||
|
|
|
|||
|
|
@ -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]);
|
||||
a_hb_one = force->numeric(FLERR,arg[3]);
|
||||
cut_hb_0_one = force->numeric(FLERR,arg[4]);
|
||||
cut_hb_c_one = force->numeric(FLERR,arg[5]);
|
||||
cut_hb_lo_one = force->numeric(FLERR,arg[6]);
|
||||
cut_hb_hi_one = force->numeric(FLERR,arg[7]);
|
||||
if (strcmp(arg[2], "seqav") != 0 && strcmp(arg[2], "seqdep") != 0) {
|
||||
error->all(FLERR,"Incorrect setting, select seqav or seqdep in oxdna/hbond");
|
||||
}
|
||||
if (strcmp(arg[2],"seqav") == 0) seqdepflag = 0;
|
||||
if (strcmp(arg[2],"seqdep") == 0) seqdepflag = 1;
|
||||
|
||||
a_hb1_one = force->numeric(FLERR,arg[8]);
|
||||
theta_hb1_0_one = force->numeric(FLERR,arg[9]);
|
||||
dtheta_hb1_ast_one = force->numeric(FLERR,arg[10]);
|
||||
epsilon_hb_one = force->numeric(FLERR,arg[3]);
|
||||
a_hb_one = force->numeric(FLERR,arg[4]);
|
||||
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]);
|
||||
theta_hb2_0_one = force->numeric(FLERR,arg[12]);
|
||||
dtheta_hb2_ast_one = force->numeric(FLERR,arg[13]);
|
||||
a_hb1_one = force->numeric(FLERR,arg[9]);
|
||||
theta_hb1_0_one = force->numeric(FLERR,arg[10]);
|
||||
dtheta_hb1_ast_one = force->numeric(FLERR,arg[11]);
|
||||
|
||||
a_hb3_one = force->numeric(FLERR,arg[14]);
|
||||
theta_hb3_0_one = force->numeric(FLERR,arg[15]);
|
||||
dtheta_hb3_ast_one = force->numeric(FLERR,arg[16]);
|
||||
a_hb2_one = force->numeric(FLERR,arg[12]);
|
||||
theta_hb2_0_one = force->numeric(FLERR,arg[13]);
|
||||
dtheta_hb2_ast_one = force->numeric(FLERR,arg[14]);
|
||||
|
||||
a_hb4_one = force->numeric(FLERR,arg[17]);
|
||||
theta_hb4_0_one = force->numeric(FLERR,arg[18]);
|
||||
dtheta_hb4_ast_one = force->numeric(FLERR,arg[19]);
|
||||
a_hb3_one = force->numeric(FLERR,arg[15]);
|
||||
theta_hb3_0_one = force->numeric(FLERR,arg[16]);
|
||||
dtheta_hb3_ast_one = force->numeric(FLERR,arg[17]);
|
||||
|
||||
a_hb7_one = force->numeric(FLERR,arg[20]);
|
||||
theta_hb7_0_one = force->numeric(FLERR,arg[21]);
|
||||
dtheta_hb7_ast_one = force->numeric(FLERR,arg[22]);
|
||||
a_hb4_one = force->numeric(FLERR,arg[18]);
|
||||
theta_hb4_0_one = force->numeric(FLERR,arg[19]);
|
||||
dtheta_hb4_ast_one = force->numeric(FLERR,arg[20]);
|
||||
|
||||
a_hb8_one = force->numeric(FLERR,arg[23]);
|
||||
theta_hb8_0_one = force->numeric(FLERR,arg[24]);
|
||||
dtheta_hb8_ast_one = force->numeric(FLERR,arg[25]);
|
||||
a_hb7_one = force->numeric(FLERR,arg[21]);
|
||||
theta_hb7_0_one = force->numeric(FLERR,arg[22]);
|
||||
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];
|
||||
|
|
|
|||
|
|
@ -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();
|
||||
};
|
||||
|
||||
|
|
|
|||
|
|
@ -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)
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||||
|
|
@ -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];
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||||
|
||||
|
|
@ -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]);
|
||||
cut_st_0_one = force->numeric(FLERR,arg[4]);
|
||||
cut_st_c_one = force->numeric(FLERR,arg[5]);
|
||||
cut_st_lo_one = force->numeric(FLERR,arg[6]);
|
||||
cut_st_hi_one = force->numeric(FLERR,arg[7]);
|
||||
a_st_one = force->numeric(FLERR,arg[4]);
|
||||
cut_st_0_one = force->numeric(FLERR,arg[5]);
|
||||
cut_st_c_one = force->numeric(FLERR,arg[6]);
|
||||
cut_st_lo_one = force->numeric(FLERR,arg[7]);
|
||||
cut_st_hi_one = force->numeric(FLERR,arg[8]);
|
||||
|
||||
a_st4_one = force->numeric(FLERR,arg[8]);
|
||||
theta_st4_0_one = force->numeric(FLERR,arg[9]);
|
||||
dtheta_st4_ast_one = force->numeric(FLERR,arg[10]);
|
||||
a_st5_one = force->numeric(FLERR,arg[11]);
|
||||
theta_st5_0_one = force->numeric(FLERR,arg[12]);
|
||||
dtheta_st5_ast_one = force->numeric(FLERR,arg[13]);
|
||||
a_st6_one = force->numeric(FLERR,arg[14]);
|
||||
theta_st6_0_one = force->numeric(FLERR,arg[15]);
|
||||
dtheta_st6_ast_one = force->numeric(FLERR,arg[16]);
|
||||
a_st1_one = force->numeric(FLERR,arg[17]);
|
||||
cosphi_st1_ast_one = force->numeric(FLERR,arg[18]);
|
||||
a_st2_one = force->numeric(FLERR,arg[19]);
|
||||
cosphi_st2_ast_one = force->numeric(FLERR,arg[20]);
|
||||
a_st4_one = force->numeric(FLERR,arg[9]);
|
||||
theta_st4_0_one = force->numeric(FLERR,arg[10]);
|
||||
dtheta_st4_ast_one = force->numeric(FLERR,arg[11]);
|
||||
a_st5_one = force->numeric(FLERR,arg[12]);
|
||||
theta_st5_0_one = force->numeric(FLERR,arg[13]);
|
||||
dtheta_st5_ast_one = force->numeric(FLERR,arg[14]);
|
||||
a_st6_one = force->numeric(FLERR,arg[15]);
|
||||
theta_st6_0_one = force->numeric(FLERR,arg[16]);
|
||||
dtheta_st6_ast_one = force->numeric(FLERR,arg[17]);
|
||||
a_st1_one = force->numeric(FLERR,arg[18]);
|
||||
cosphi_st1_ast_one = force->numeric(FLERR,arg[19]);
|
||||
a_st2_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];
|
||||
|
|
|
|||
|
|
@ -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();
|
||||
};
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue