\(\renewcommand{\AA}{\text{Å}}\)
pair_style oxdna3/excv command
pair_style oxdna3/stk command
pair_style oxdna3/hbond command
pair_style oxdna3/xstk command
pair_style oxdna3/coaxstk command
pair_style oxdna3/dh command
Syntax
pair_style style1
pair_coeff * * style2 args (keyword value)
style1 = hybrid/overlay oxdna3/excv oxdna3/stk oxdna3/hbond oxdna3/xstk oxdna3/coaxstk oxdna3/dh
style2 = oxdna3/excv or oxdna3/stk or oxdna3/hbond or oxdna3/xstk or oxdna3/coaxstk or oxdna3/dh
args = list of arguments for these particular styles
zero or one keyword/value pair may be appended to oxdna3/dh
keyword = half_charged_ends
oxdna3/excv args = oxdna3_lj.cgdna or oxdna3_real.cgdna oxdna3/stk args = T oxdna3_lj.cgdna or oxdna3_real.cgdna T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K) oxdna3/hbond args = oxdna3_lj.cgdna or oxdna3_real.cgdna oxdna3/xstk args = oxdna3_lj.cgdna or oxdna3_real.cgdna oxdna3/coaxstk args = oxdna3_lj.cgdna or oxdna3_real.cgdna oxdna3/dh args [keyword value] = T rhos oxdna3_lj.cgdna or oxdna3_real.cgdna [half_charged_ends no|yes] T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K) rhos = salt concentration (mole per litre) half_charged_ends yes = set half charge at terminal nucleotides half_charged_ends no = set full charge at terminal nucleotides
Examples
# LJ units
pair_style hybrid/overlay oxdna3/excv oxdna3/stk oxdna3/hbond oxdna3/xstk oxdna3/coaxstk oxdna3/dh
pair_coeff * * oxdna3/excv oxdna3_lj.cgdna
pair_coeff * * oxdna3/stk 0.1 oxdna3_lj.cgdna
pair_coeff * * oxdna3/hbond oxdna3_lj.cgdna
pair_coeff 1 4 oxdna3/hbond oxdna3_lj.cgdna
pair_coeff 2 3 oxdna3/hbond oxdna3_lj.cgdna
pair_coeff * * oxdna3/xstk oxdna3_lj.cgdna
pair_coeff * * oxdna3/coaxstk oxdna3_lj.cgdna
pair_coeff * * oxdna3/dh 0.1 0.2 oxdna3_lj.cgdna
# Real units
pair_style hybrid/overlay oxdna3/excv oxdna3/stk oxdna3/hbond oxdna3/xstk oxdna3/coaxstk oxdna3/dh
pair_coeff * * oxdna3/excv oxdna3_real.cgdna
pair_coeff * * oxdna3/stk 300.0 oxdna3_real.cgdna
pair_coeff * * oxdna3/hbond oxdna3_real.cgdna
pair_coeff 1 4 oxdna3/hbond oxdna3_real.cgdna
pair_coeff 2 3 oxdna3/hbond oxdna3_real.cgdna
pair_coeff * * oxdna3/xstk oxdna3_real.cgdna
pair_coeff * * oxdna3/coaxstk oxdna3_real.cgdna
pair_coeff * * oxdna3/dh 300.0 0.2 oxdna3_real.cgdna
Note
The coefficients are provided in forms compatible with both
units lj and units real. The potential file unit system
must align with the units defined via the units command.
In case of oxDNA3 almost all coefficients have to be read from a potential
file with correct unit style by specifying the name of the file. The
potential files for each unit style are included in the potentials
directory of the LAMMPS distribution.
Description
Added in version 30Mar2026.
The oxdna3 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 oxdna3/excv, the stacking oxdna3/stk, cross-stacking oxdna3/xstk and coaxial stacking interaction oxdna3/coaxstk, electrostatic Debye-Hueckel interaction oxdna3/dh as well as the hydrogen-bonding interaction oxdna3/hbond between complementary pairs of nucleotides on opposite strands.
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 (Bonato) and the original oxDNA publications (Ouldridge-DPhil) and (Ouldridge) for a detailed description of the oxDNA3 force field.
Note
These pair styles have to be used together with the related oxDNA3 bond style oxdna3/fene for the connectivity of the phosphate backbone (see also documentation of bond_style oxdna3/fene). All coefficients in the above mentioned potential files have to be kept fixed and cannot be changed without reparameterizing the entire model. The first coefficient after oxdna3/stk (T=0.1 and corresponding real unit equivalents in the above examples) and the two coefficients after oxdna3/dh (T=0.1 and rhos=0.2 in the above example) have to be set to the temperature and salt concentration of the system. oxdna3/dh has the option to set half a charge at terminal nucleotides (half_charged_ends yes) to aid coaxial stacking. 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/oxDNA3/ 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/.
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 oxDNA3 publication (Bonato).
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
The option default is half_charged_ends = no.
(Bonato) A. Bonato, T.E. Ouldridge, A.A. Louis, J.P.K. Doye, L. Rovigatti, M. Matthies, O.Henrich, in preparation.
(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).
(Henrich) O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).