"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)

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pair_style oxdna/excv command :h3
pair_style oxdna/stk command :h3
pair_style oxdna/hbond command :h3
pair_style oxdna/xstk command :h3
pair_style oxdna/coaxstk command :h3

[Syntax:]

pair_style style1 :pre

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

  {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

[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/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

[Description:]

The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
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.

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,
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
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
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).
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.

Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
A simple python setup tool which creates single straight or helical DNA strands,
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
A technical report with more information on the model, the structure of the input file,
the setup tool and the performance of the LAMMPS-implementation of oxDNA
can be found "here"_PDF/USER-CGDNA-overview.pdf.

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[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
LAMMPS"_Section_start.html#start_3 section for more info on packages.

[Related commands:]

"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
"bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html

[Default:] none

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: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).