Modified initialisation of sequence-dependent stacking and h-bonding strength (d1581f20) · Commits · 郑智淋 / lammps

src/USER-CGDNA/pair_oxdna_hbond.cpp

+24 −8

Original line number	Diff line number	Diff line
		@@ -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 −0

Original line number	Diff line number	Diff line
		@@ -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;

+24 −8

Original line number	Diff line number	Diff line
		@@ -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 −0

Original line number	Diff line number	Diff line
		@@ -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;