Commit 4161868b authored by Steve Plimpton's avatar Steve Plimpton Committed by GitHub
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Merge pull request #640 from ohenrich/user-cgdna 

USER-CGDNA - sequence-dependent stacking and h-bonding strength
parents 9ca39c89 c8967a33

doc/src/PDF/USER-CGDNA-overview.pdf

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doc/src/fix_nve_dot.txt

+1 −1
Original line number Diff line number Diff line
@@ -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

+11 −4
Original line number Diff line number Diff line
@@ -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

+23 −13
Original line number Diff line number Diff line
@@ -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}

args = list of arguments for these two particular styles :ul

style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}

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

    T = temperature (oxDNA units, 0.1 = 300 K) :pre

  {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

    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/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     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   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 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

in the above example. The individual potentials consist of products of modulation factors,

The exact functional form of the pair styles is rather complex.

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

+19 −10
Original line number Diff line number Diff line
@@ -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}

args = list of arguments for these two particular styles :ul

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



  {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/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     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   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 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).

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