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Modified initialisation of sequence-dependent stacking and h-bonding strength

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This commit is contained in:
Oliver Henrich
2019-10-17 15:26:32 +01:00
parent 44fb441f99
commit d1581f20a9
4 changed files with 50 additions and 16 deletions
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32
src/USER-CGDNA/pair_oxdna_hbond.cpp
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@ -32,20 +32,36 @@
using namespace LAMMPS_NS;
using namespace MFOxdna;
// sequence-specific base-pairing strength
// A:0 C:1 G:2 T:3, 5'- (i,j) -3'
static const double alpha_hb[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)
{
single_enable = 0;
writedata = 1;
// sequence-specific base-pairing strength
// A:0 C:1 G:2 T:3, 5'- [i][j] -3'
alpha_hb[0][0] = 1.00000;
alpha_hb[0][1] = 1.00000;
alpha_hb[0][2] = 1.00000;
alpha_hb[0][3] = 0.82915;
alpha_hb[1][0] = 1.00000;
alpha_hb[1][1] = 1.00000;
alpha_hb[1][2] = 1.15413;
alpha_hb[1][3] = 1.00000;
alpha_hb[2][0] = 1.00000;
alpha_hb[2][1] = 1.15413;
alpha_hb[2][2] = 1.00000;
alpha_hb[2][3] = 1.00000;
alpha_hb[3][0] = 0.82915;
alpha_hb[3][1] = 1.00000;
alpha_hb[3][2] = 1.00000;
alpha_hb[3][3] = 1.00000;
}
/* ---------------------------------------------------------------------- */

1
src/USER-CGDNA/pair_oxdna_hbond.h
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@ -45,6 +45,7 @@ class PairOxdnaHbond : public Pair {
protected:
// h-bonding interaction
double alpha_hb[4][4];
double **epsilon_hb, **a_hb, **cut_hb_0, **cut_hb_c, **cut_hb_lo, **cut_hb_hi;
double **cut_hb_lc, **cut_hb_hc, **b_hb_lo, **b_hb_hi, **shift_hb;
double **cutsq_hb_hc;

32
src/USER-CGDNA/pair_oxdna_stk.cpp
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@ -32,20 +32,36 @@
using namespace LAMMPS_NS;
using namespace MFOxdna;
// sequence-specific stacking strength
// A:0 C:1 G:2 T:3, 5'- (i,j) -3'
static const double eta_st[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)
{
single_enable = 0;
writedata = 1;
// sequence-specific stacking strength
// A:0 C:1 G:2 T:3, 5'- [i][j] -3'
eta_st[0][0] = 1.11960;
eta_st[0][1] = 1.00852;
eta_st[0][2] = 0.96950;
eta_st[0][3] = 0.99632;
eta_st[1][0] = 1.01889;
eta_st[1][1] = 0.97804;
eta_st[1][2] = 1.02681;
eta_st[1][3] = 0.96950;
eta_st[2][0] = 0.98169;
eta_st[2][1] = 1.05913;
eta_st[2][2] = 0.97804;
eta_st[2][3] = 1.00852;
eta_st[3][0] = 0.94694;
eta_st[3][1] = 0.98169;
eta_st[3][2] = 1.01889;
eta_st[3][3] = 0.96383;
}
/* ---------------------------------------------------------------------- */

1
src/USER-CGDNA/pair_oxdna_stk.h
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@ -45,6 +45,7 @@ class PairOxdnaStk : public Pair {
protected:
// stacking interaction
double eta_st[4][4];
double stacking_strength(double, double, double);
double **epsilon_st, **a_st, **cut_st_0, **cut_st_c;
double **cut_st_lo, **cut_st_hi;