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lammps/doc/src/pair_oxdna2.txt
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"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)
:line
pair_style oxdna2/excv command :h3
pair_style oxdna2/stk command :h3
pair_style oxdna2/hbond command :h3
pair_style oxdna2/xstk command :h3
pair_style oxdna2/coaxstk command :h3
pair_style oxdna2/dh command :h3
[Syntax:]
pair_style style1 :pre
pair_coeff * * style2 args :pre
style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh} :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 = 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)
qeff = effective charge (elementary charges) :pre
[Examples:]
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 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
[Description:]
The {oxdna2} 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 {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. 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,
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 "(Snodin)"_#Snodin and the original oxDNA publications "(Ouldridge-DPhil)"_#Ouldridge-DPhil2
and "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force field.
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). 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 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.
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.
:line
[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 oxdna2/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html
[Default:] none
: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).
:link(Ouldridge-DPhil2)
[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
:link(Ouldridge2)
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
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