pair_style oxdna/excv command

pair_style oxdna/stk command

pair_style oxdna/hbond command

pair_style oxdna/xstk command

pair_style oxdna/coaxstk command

Syntax

pair_style style
  • style = hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk

Examples

pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk     1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65

Description

The oxdna pair styles compute the pairwise-additive parts of the oxDNA force field for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the excluded volume interaction oxdna/excv, the stacking oxdna/stk, cross-stacking oxdna/xstk and coaxial stacking interaction oxdna/coaxstk as well as the hydrogen-bonding interaction oxdna/hbond between complementary pairs of nucleotides on opposite strands.

The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients in the above example. The individual potentials consist of products of modulation factors, which themselves are constructed from a number of more basic potentials (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. We refer to (Ouldridge-DPhil) and (Ouldridge) for a detailed description of the oxDNA force field.

Note

These pair styles have to be used together with the related oxDNA bond style oxdna/fene for the connectivity of the phosphate backbone (see also documentation of bond_style oxdna/fene). 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

These pair styles 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.