Homec4science
Diffusion lammps (master) Browse

lammps/doc/src/bond_oxdna.txt
e368acdaeb22master

Last Change
Raw File

bond_oxdna.txt
View Options

"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
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 reparametrizing 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/.
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, "pair_style oxdna2/excv"_pair_oxdna2.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).
:link(oxdna2)
[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
c4science · Help