pair_style oxdna2/excv command

pair_style oxdna2/stk command

pair_style oxdna2/hbond command

pair_style oxdna2/xstk command

pair_style oxdna2/coaxstk command

pair_style oxdna2/dh command

Syntax

pair_style style1

pair_coeff * * style2 args

• style1 = hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh

• style2 = oxdna2/excv or oxdna2/stk or oxdna2/hbond or oxdna2/xstk or oxdna2/coaxstk or oxdna2/dh

• args = list of arguments for these particular styles

oxdna2/stk args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
  seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
  T = temperature (oxDNA units, 0.1 = 300 K)
  xi = 1.3523 (temperature-independent coefficient in stacking strength)
  kappa = 2.6717 (coefficient of linear temperature dependence in stacking strength)
oxdna2/hbond args = seq eps 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
  seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
  eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
oxdna2/dh args = T rhos qeff
  T = temperature (oxDNA units, 0.1 = 300 K)
  rhos = salt concentration (mole per litre)
  qeff = 0.815 (effective charge in elementary charges)

Examples

pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 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 * * oxdna2/hbond   seqdep 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 oxdna2/hbond   seqdep 1.0678 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 oxdna2/hbond   seqdep 1.0678 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 * * oxdna2/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 * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh      0.1 0.5 0.815

Description

The oxdna2 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 oxdna2/excv, the stacking oxdna2/stk, cross-stacking oxdna2/xstk and coaxial stacking interaction oxdna2/coaxstk, electrostatic Debye-Hueckel interaction oxdna2/dh as well as the hydrogen-bonding interaction oxdna2/hbond between complementary pairs of nucleotides on opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths are supported (Sulc). Quasi-unique base-pairing between nucleotides can be achieved by using more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. This prevents the hybridization of in principle complementary bases within Ntypes/4 bases up and down along the backbone.

The exact functional form of the pair styles is rather complex. 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 (Snodin) and the original oxDNA publications (Ouldridge-DPhil) and (Ouldridge) for a detailed description of the oxDNA2 force field.

Note

These pair styles have to be used together with the related oxDNA2 bond style oxdna2/fene for the connectivity of the phosphate backbone (see also documentation of bond_style oxdna2/fene). Most of the coefficients in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. Exceptions are the first four coefficients after oxdna2/stk (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example), the first coefficient after oxdna2/hbond (seq=seqdep in the above example) and the three coefficients after oxdna2/dh (T=0.1, rhos=0.5, qeff=0.815 in the above example). When using a Langevin thermostat e.g. through fix langevin or fix nve/dotc/langevin the temperature coefficients have to be matched to the one used in the fix.

Note

These pair styles have to be used with the atom_style hybrid bond ellipsoid oxdna (see documentation of atom_style). The atom_style oxdna stores the 3’-to-5’ polarity of the nucleotide strand, which is set through the bond topology in the data file. The first (second) atom in a bond definition is understood to point towards the 3’-end (5’-end) of the strand.

Example input and data files for DNA duplexes can be found in examples/PACKAGES/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/PACKAGES/cgdna/util/.

Please cite (Henrich) in any publication that uses this implementation. The article contains general information on the model, its implementation and performance as well as the structure of the data and input file. The preprint version of the article can be found here. Please cite also the relevant oxDNA2 publications (Snodin) and (Sulc).

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Restrictions

These pair styles can only be used if LAMMPS was built with the CG-DNA package and the MOLECULE and ASPHERE package. See the Build package page for more info.

Related commands

bond_style oxdna2/fene, pair_coeff, bond_style oxdna/fene, pair_style oxdna/excv, bond_style oxrna2/fene, pair_style oxrna2/excv, atom_style oxdna, fix nve/dotc/langevin

Default

none

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(Henrich) O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).

(Snodin) B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).

(Sulc) P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).

(Ouldridge-DPhil) T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).

(Ouldridge) T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).