bond_style oxdna/fene command

Syntax

bond_style oxdna/fene

Examples

bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525

Description

The oxdna/fene bond style uses the potential

_images/bond_oxdna_fene.jpg

to define a modified finite extensible nonlinear elastic (FENE) potential (Ouldridge) 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 command as given in the above example, or in the data file or restart files read by the read_data or read_restart commands:

  • epsilon (energy)
  • Delta (distance)
  • r0 (distance)

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). 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.


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 for more info on packages.