\(\renewcommand{\AA}{\text{Å}}\)
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 1.3448 2.6568 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 8.01727944817084 0.005279604 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). 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 (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 four coefficients after oxdna/stk (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 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.
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 oxDNA publications (Ouldridge), (Ouldridge-DPhil) and (Sulc).
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/
.
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).