\(\renewcommand{\AA}{\text{Å}}\)

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 style1

pair_coeff * * style2 args

  • style1 = hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk

  • style2 = oxdna/excv or oxdna/stk or oxdna/hbond or oxdna/xstk or oxdna/coaxstk

  • args = list of arguments for these particular styles

oxdna/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 = 1.3448 (LJ units) or 8.01727944817084 (real units), temperature-independent coefficient in stacking strength
  kappa = 2.6568 (LJ units) or 0.005279604 (real units), coefficient of linear temperature dependence in stacking strength
oxdna/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 = 1.077 (LJ units) or 6.42073911784652 (real units), average hydrogen bonding strength between A-T and C-G Watson-Crick base pairs, 0 between all other pairs

Examples

# LJ units
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     seqdep 0.1 1.3448 2.6568 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 * * oxdna/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 oxdna/hbond   seqdep 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   seqdep 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

pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv    oxdna_lj.cgdna
pair_coeff * * oxdna/stk     seqav 0.1 oxdna_lj.cgdna
pair_coeff * * oxdna/hbond   seqav oxdna_lj.cgdna
pair_coeff 1 4 oxdna/hbond   seqav oxdna_lj.cgdna
pair_coeff 2 3 oxdna/hbond   seqav oxdna_lj.cgdna
pair_coeff * * oxdna/xstk    oxdna_lj.cgdna
pair_coeff * * oxdna/coaxstk oxdna_lj.cgdna

# Real units
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv    11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
pair_coeff * * oxdna/stk     seqdep 300.0 8.01727944817084 0.005279604 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 * * oxdna/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 oxdna/hbond   seqdep 6.42073911784652 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 oxdna/hbond   seqdep 6.42073911784652 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 * * oxdna/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 * * oxdna/coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 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_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv    oxdna_real.cgdna
pair_coeff * * oxdna/stk     seqav 300.0 oxdna_real.cgdna
pair_coeff * * oxdna/hbond   seqav oxdna_real.cgdna
pair_coeff 1 4 oxdna/hbond   seqav oxdna_real.cgdna
pair_coeff 2 3 oxdna/hbond   seqav oxdna_real.cgdna
pair_coeff * * oxdna/xstk    oxdna_real.cgdna
pair_coeff * * oxdna/coaxstk oxdna_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 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. Average sequence or sequence-dependent stacking and base-pairing strengths are supported (Sulc).

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 (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). 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 two coefficients after oxdna/stk (seq=seqdep and T=0.1 and corresponding real unit equivalents in the above examples) and the first coefficient after oxdna/hbond (seq=seqdep 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.

Warning

If data files are produced with write_data, then the newton command should be set to newton on. Otherwise the data files will not have the same 3’-to-5’ polarity as the initial data file. This limitation does not apply to binary restart files produced with write_restart.

Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/lj_units/oxDNA/ or in the corresponding folder for real units. 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/.

Potential file reading

For each pair style above the first non-modifiable argument can be a filename, and if it is, no further arguments should be supplied. Therefore the following command:

pair_coeff 1 4 oxdna/hbond   seqav oxdna_lj.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 oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv    oxdna_lj.cgdna
pair_coeff * * oxdna/stk     seqav 0.1 1.3448 2.6568 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 * * oxdna/hbond   seqav oxdna_lj.cgdna
pair_coeff 1 4 oxdna/hbond   seqav oxdna_lj.cgdna
pair_coeff 2 3 oxdna/hbond   seqav oxdna_lj.cgdna
pair_coeff * * oxdna/xstk    oxdna_lj.cgdna
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

will read the stacking and coaxial stacking potential parameters from the manual specification and all others from the potential file oxdna_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/.

Unique base pairing

Unique base pairing describes the restriction on the specific complementary nucleotide with which a particular base can pair. This can be used to prevent asymmetric base pairs or to simplify the free energy landscape. With unique base pairing enabled base pairs can only form between complementary nucleotides with specific atom IDs. This functionality draws on fix property/atom and a modified read_data command.

To use unique base pairing, the data file of a system with N nucleotides must contain a section like

Basepairs # i_idc

1 idc1
2 idc2
3 idc3
4 idc4
...
N idcN

where idc is the non-negative atom ID of a complementary nucleotide that binds uniquely to the preceding atom ID.

Unique base pairing can be combined with normal base pairing by setting a zero or negative value for idc. For instance, in a 4-mer with 8 nucleotides consisting of a ssDNA strand 3’-A-A-A-A-5’ with atom IDs 3’-1-2-3-4-5’ and a complementary strand 5’-T-T-T-T-3’ with atom IDs 5’-8-7-6-5-3’ set up as

Basepairs # i_idc

1 8
2 -1
3 -1
4 5
5 4
6 -1
7 -1
8 1

the A nucleotide with ID 1 can only hybridize with the T nucleotide with ID 8 and the A nucleotide with ID 4 can only hybridize with the T nucleotide with ID 5, whereas the A nucleotides with ID 2 and 3 can hybridize with either T nucleotide with ID 6 and 7.

The input file requires an instance of the fix property/atom and a read_data command as follows:

fix Basepairs all property/atom i_idc ghost yes
read_data file fix Basepairs NULL Basepairs

where file is the name of the data file and the only modifiable argument. An example input and data file for a dsDNA ring can be found in examples/PACKAGES/cgdna/examples/lj_units/oxDNA3/unique_bp or in the corresponding folder for real units.

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 oxDNA publications (Ouldridge), (Ouldridge-DPhil) and (Sulc).

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.

Default

none

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

(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).

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