Merge pull request #1573 from ohenrich/user-cgdna (67b74aea) · Commits · 郑智淋 / lammps

doc/src/PDF/USER-CGDNA.pdf

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doc/src/pair_oxdna.txt

+5 −3

doc/src/pair_oxdna2.txt

+7 −5

examples/USER/cgdna/README

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Original line number	Original line	Diff line number	Diff line
	@@ -22,6 +22,17 @@ A - C - G - T - A - C - G - T
	\| \| \| \| \| \| \| \|		\| \| \| \| \| \| \| \|
	T - G - C - A T - G - C - A		T - G - C - A T - G - C - A

			/examples/duplex3:
			This is basically the duplex1 run with sequence-dependent stacking
			and hydrogen-bonding strengths enabled and both nucleotide mass and
			moment of inertia set to the value of the standalone implementation
			of oxDNA (M = I = 1). To achieve this, the masses can be set directly
			in the input and data file, whereas the moment of inertia is set via
			the diameter of the ellipsoid in the data file and has a value of 3.16227766.
			The change of mass and moment of inertia allows direct comparision of
			e.g. trajectory data, energies or time-dependent observables on a per-timestep
			basis until numerical noise causes deviations at later simulation times.

	/util:		/util:
	This directory contains a simple python setup tool which creates		This directory contains a simple python setup tool which creates
	single straight or helical DNA strands, DNA duplexes or arrays of DNA		single straight or helical DNA strands, DNA duplexes or arrays of DNA

examples/USER/cgdna/examples/oxDNA/duplex1/data.duplex1

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -32,7 +32,7 @@ Atoms
	9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1		9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
	10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1		10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1

	# Atom-ID, translational, rotational velocity		# Atom-ID, translational velocity, angular momentum
	Velocities		Velocities

	1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00		1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00

Original line number	Original line	Diff line number	Diff line
	@@ -23,9 +23,11 @@ style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxs
	style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}		style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
	args = list of arguments for these particular styles :ul		args = list of arguments for these particular styles :ul

	{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		{oxdna/stk} args = seq T xi kappa 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)		seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
	T = temperature (oxDNA units, 0.1 = 300 K)		T = temperature (oxDNA units, 0.1 = 300 K)
			xi = temperature-independent coefficient in stacking strength
			kappa = coefficient of linear temperature dependence in stacking strength
	{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		{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)		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		eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre
	@@ -34,7 +36,7 @@ args = list of arguments for these particular styles :ul

	pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk		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/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
	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/stk seqdep 0.1 1.3448 2.6568 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 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 * * 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 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 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 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 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
	@@ -62,7 +64,7 @@ NOTE: These pair styles have to be used together with the related oxDNA bond sty
	{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of		{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
	"bond_style oxdna/fene"_bond_oxdna.html). Most of 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 reparameterizing the entire model.		in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
	Exceptions are the first and second coefficient after {oxdna/stk} (seq=seqdep and T=0.1 in the above example)		Exceptions are the first four coefficients after {oxdna/stk} (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example)
	and the first coefficient after {oxdna/hbond} (seq=seqdep 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		When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
	or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html		or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html

Original line number	Original line	Diff line number	Diff line
	@@ -24,10 +24,12 @@ style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/
	style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} 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 particular styles :ul		args = list of arguments for these particular styles :ul

	{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		{oxdna2/stk} args = seq T xi kappa 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)		seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
	T = temperature (oxDNA units, 0.1 = 300 K)		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		xi = temperature-independent coefficient in stacking strength
			kappa = coefficient of linear temperature dependence in stacking strength
			{oxdna2/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)		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)		eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
	{oxdna2/dh} args = T rhos qeff		{oxdna2/dh} args = T rhos qeff
	@@ -39,7 +41,7 @@ args = list of arguments for these particular styles :ul

	pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh		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/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
	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/stk seqdep 0.1 1.3523 2.6717 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 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 * * 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 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 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 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 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
	@@ -68,8 +70,8 @@ NOTE: These pair styles have to be used together with the related oxDNA2 bond st
	{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of		{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
	"bond_style oxdna2/fene"_bond_oxdna.html). Most of the 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 reparameterizing the entire model.		in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
	Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example),		Exceptions are the first four coefficients after {oxdna2/stk} (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
	the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients		the first coefficient after {oxdna2/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		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		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.		the temperature coefficients have to be matched to the one used in the fix.

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