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

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

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bond_style oxdna/fene command :h3
bond_style oxdna2/fene command :h3

[Syntax:]

bond_style oxdna/fene :pre
bond_style oxdna2/fene :pre

[Examples:]

bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525 :pre

bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564 :pre

[Description:]

The {oxdna/fene} and {oxdna2/fene} bond styles use the potential

:c,image(Eqs/bond_oxdna_fene.jpg)

to define a modified finite extensible nonlinear elastic (FENE)
potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the
phosphate backbone in the oxDNA force field for coarse-grained
modelling of DNA.

The following coefficients must be defined for the bond type via the
"bond_coeff"_bond_coeff.html command as given in the above example, or
in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:

epsilon (energy)
Delta (distance)
r0 (distance) :ul

NOTE: The oxDNA bond style has to be used together with the
corresponding oxDNA pair styles for excluded volume interaction
{oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and
coaxial stacking interaction {oxdna/coaxstk} as well as
hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2
"(Snodin)"_#oxdna2 bond style the analogous pair styles and an
additional Debye-Hueckel pair style {oxdna2/dh} have to be defined.
The coefficients in the above example have to be kept fixed and cannot
be changed without reparameterizing the entire model.

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/.

Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in
any publication that uses this implementation.  The article contains
more information on the model, the structure of the input file, the
setup tool and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found
"here"_PDF/USER-CGDNA.pdf.

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[Restrictions:]

This bond style can only be used if LAMMPS was built with the
USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
"Build package"_Build_package.html doc page for more info.

[Related commands:]

"pair_style oxdna/excv"_pair_oxdna.html, "pair_style
oxdna2/excv"_pair_oxdna2.html, "fix
nve/dotc/langevin"_fix_nve_dotc_langevin.html,
"bond_coeff"_bond_coeff.html

[Default:] none

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:link(Henrich2)
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk,
T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).

:link(oxdna_fene)
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye,
J. Chem. Phys. 134, 085101 (2011).

:link(oxdna2)
[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
J. Chem. Phys. 142, 234901 (2015).
