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lammps/doc/src/bond_oxdna.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
bond_style oxdna/fene command :h3
[Syntax:]
bond_style oxdna/fene :pre
[Examples:]
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525 :pre
[Description:]
The {oxdna/fene} bond style uses 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: This 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). The coefficients
in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
Example input and data files can be found in examples/USER/cgdna/examples/duplex1/ and /duplex2/.
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:]
This bond style 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:]
"pair_style oxdna/excv"_pair_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
[Default:] none
:line
:link(oxdna_fene)
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
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