pair_style oxdna2/excv command — LAMMPS documentation

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# 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 (LJ units: 0.1 = 300 K, real units: 300 = 300 K)
      xi = 1.3523 (LJ units) or 8.06199211612242 (real units), temperature-independent coefficient in stacking strength
      kappa = 2.6717 (LJ units) or 0.005309213 (real units), 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 (LJ units) or 6.36589157849259 (real units), average hydrogen bonding strength between A-T and C-G Watson-Crick base pairs, 0 between all other pairs
    oxdna2/dh args = T rhos qeff
      T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K)
      rhos = salt concentration (mole per litre)
      qeff = 0.815 (effective charge in elementary charges)

## Examples

    # LJ units
    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

    pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
    pair_coeff * * oxdna2/excv    oxdna2_lj.cgdna
    pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 oxdna2_lj.cgdna
    pair_coeff * * oxdna2/hbond   seqdep oxdna2_lj.cgdna
    pair_coeff 1 4 oxdna2/hbond   seqdep oxdna2_lj.cgdna
    pair_coeff 2 3 oxdna2/hbond   seqdep oxdna2_lj.cgdna
    pair_coeff * * oxdna2/xstk    oxdna2_lj.cgdna
    pair_coeff * * oxdna2/coaxstk oxdna2_lj.cgdna
    pair_coeff * * oxdna2/dh      0.1 0.5 oxdna2_lj.cgdna

    # Real units
    pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
    pair_coeff * * oxdna2/excv    11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
    pair_coeff * * oxdna2/stk     seqdep 300.0 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
    pair_coeff * * oxdna2/hbond   seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
    pair_coeff 1 4 oxdna2/hbond   seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
    pair_coeff 2 3 oxdna2/hbond   seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
    pair_coeff * * oxdna2/xstk    3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0.0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
    pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 40.0 3.116592653589793
    pair_coeff * * oxdna2/dh      300.0 0.5 0.815

    pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
    pair_coeff * * oxdna2/excv    oxdna2_real.cgdna
    pair_coeff * * oxdna2/stk     seqdep 300.0 8.06199211612242 0.005309213 oxdna2_real.cgdna
    pair_coeff * * oxdna2/hbond   seqdep oxdna2_real.cgdna
    pair_coeff 1 4 oxdna2/hbond   seqdep oxdna2_real.cgdna
    pair_coeff 2 3 oxdna2/hbond   seqdep oxdna2_real.cgdna
    pair_coeff * * oxdna2/xstk    oxdna2_real.cgdna
    pair_coeff * * oxdna2/coaxstk oxdna2_real.cgdna
    pair_coeff * * oxdna2/dh      300.0 0.5 oxdna2_real.cgdna

Note

The coefficients in the above examples are provided in forms compatible with both units lj and units real (see documentation of units). These can also be read from a potential file with correct unit style by specifying the name of the file. Several potential files for each unit style are included in the `potentials` directory of the LAMMPS distribution.

## 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 and corresponding real unit equivalents in the above examples). 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. An updated documentation that contains general information on the model, its implementation and performance as well as the structure of the data and input file can be found here.

Please cite also the relevant oxDNA2 publications (Snodin) and (Sulc).

## Potential file reading

For each pair style above the first non-modifiable argument can be a filename (with exception of Debye-Hueckel, for which the effective charge argument can be a filename), and if it is, no further arguments should be supplied. Therefore the following command:

    pair_coeff 1 4 oxdna2/hbond   seqdep oxdna_real.cgdna

will be interpreted as a request to read the corresponding hydrogen bonding potential parameters from the file with the given name. The file can define multiple potential parameters for both bonded and pair interactions, but for the example pair interaction above there must exist in the file a line of the form:

    1 4 hbond     <coefficients>

If potential customization is required, the potential file reading can be mixed with the manual specification of the potential parameters. For example, the following command:

    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 oxdna2_lj.cgdna
    pair_coeff * * oxdna2/hbond   seqdep oxdna2_lj.cgdna
    pair_coeff 1 4 oxdna2/hbond   seqdep oxdna2_lj.cgdna
    pair_coeff 2 3 oxdna2/hbond   seqdep oxdna2_lj.cgdna
    pair_coeff * * oxdna2/xstk    oxdna2_lj.cgdna
    pair_coeff * * oxdna2/coaxstk oxdna2_lj.cgdna
    pair_coeff * * oxdna2/dh      0.1 0.5 0.815

will read the excluded volume and Debye-Hueckel effective charge qeff parameters from the manual specification and all others from the potential file oxdna2_lj.cgdna.

There are sample potential files for each unit style in the `potentials` directory of the LAMMPS distribution. The potential file unit system must align with the units defined via the units command. For conversion between different LJ and real unit systems for oxDNA, the python tool lj2real.py located in the `examples/PACKAGES/cgdna/util/` directory can be used. This tool assumes similar file structure to the examples found in `examples/PACKAGES/cgdna/examples/`.

## 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

(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).