\(\renewcommand{\AA}{\text{Å}}\)
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 [keyword value]
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
zero or one keyword/value pair may be appended to oxdna2/dh
keyword = half_charged_ends
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 [keyword value] = T rhos qeff [half_charged_ends no|yes] 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) 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 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 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 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
Added in version 30Mar2026.
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).
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 two coefficients after oxdna2/stk (seq=seqdep and T=0.1 and corresponding real unit equivalents in the above examples), the first coefficient after oxdna2/hbond (seq=seqdep in the above example) and the two coefficients after oxdna2/dh (T=0.1 and rhos=0.5 in the above example). oxdna2/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/oxDNA2/ 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/.
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 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/.
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.
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).
(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).