bond_style oxdna/fene command

bond_style oxdna2/fene command

Syntax

bond_style oxdna/fene

bond_style oxdna2/fene

Examples

bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525

bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564

Description

The oxdna/fene and oxdna2/fene bond styles use 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

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). For the oxDNA2 (Snodin) 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.


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.