\(\renewcommand{\AA}{\text{Å}}\)

pair_style oxrna2/excv command

pair_style oxrna2/stk command

pair_style oxrna2/hbond command

pair_style oxrna2/xstk command

pair_style oxrna2/coaxstk command

pair_style oxrna2/dh command

Syntax

pair_style style1

pair_coeff * * style2 args

  • style1 = hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh

  • style2 = oxrna2/excv or oxrna2/stk or oxrna2/hbond or oxrna2/xstk or oxrna2/coaxstk or oxrna2/dh

  • args = list of arguments for these particular styles

oxrna2/stk args = seq T xi kappa 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 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 = 1.40206 (LJ units) or 8.35864576375849 (real units), temperature-independent coefficient in stacking strength
  kappa = 2.77 (LJ units) or 0.005504556 (real units), coefficient of linear temperature dependence in stacking strength
oxrna2/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 = 0.870439 (LJ units) or 5.18928666388042 (real units), average hydrogen bonding strength between A-U and C-G Watson-Crick and G-U wobble base pairs, 0 between all other pairs
oxrna2/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 = 1.02455 (effective charge in elementary charges)

Examples

# LJ units
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
pair_coeff * * oxrna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxrna2/stk     seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
pair_coeff * * oxrna2/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 oxrna2/hbond   seqdep 0.870439 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 oxrna2/hbond   seqdep 0.870439 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 3 4 oxrna2/hbond   seqdep 0.870439 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 * * oxrna2/xstk    59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
pair_coeff * * oxrna2/dh      0.1 0.5 1.02455

pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
pair_coeff * * oxrna2/excv    oxrna2_lj.cgdna
pair_coeff * * oxrna2/stk     seqdep 0.1 oxrna2_lj.cgdna
pair_coeff * * oxrna2/hbond   seqdep oxrna2_lj.cgdna
pair_coeff 1 4 oxrna2/hbond   seqdep oxrna2_lj.cgdna
pair_coeff 2 3 oxrna2/hbond   seqdep oxrna2_lj.cgdna
pair_coeff 3 4 oxrna2/hbond   seqdep oxrna2_lj.cgdna
pair_coeff * * oxrna2/xstk    oxrna2_lj.cgdna
pair_coeff * * oxrna2/coaxstk oxrna2_lj.cgdna
pair_coeff * * oxrna2/dh      0.1 0.5 oxrna2_lj.cgdna

# Real units
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
pair_coeff * * oxrna2/excv    11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
pair_coeff * * oxrna2/stk     seqdep 300.0 8.35864576375849 0.005504556 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65
pair_coeff * * oxrna2/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 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxrna2/hbond   seqdep 5.18928666388042 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 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxrna2/hbond   seqdep 5.18928666388042 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 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 3 4 oxrna2/hbond   seqdep 5.18928666388042 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 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxrna2/xstk    4.92690859644113 4.259 5.1108 3.57756 4.94044 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
pair_coeff * * oxrna2/coaxstk 6.57330882442206 4.259 5.1108 3.57756 4.94044 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
pair_coeff * * oxrna2/dh      300.0 0.5 1.02455

pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
pair_coeff * * oxrna2/excv    oxrna2_real.cgdna
pair_coeff * * oxrna2/stk     seqdep 300.0 oxrna2_real.cgdna
pair_coeff * * oxrna2/hbond   seqdep oxrna2_real.cgdna
pair_coeff 1 4 oxrna2/hbond   seqdep oxrna2_real.cgdna
pair_coeff 2 3 oxrna2/hbond   seqdep oxrna2_real.cgdna
pair_coeff 3 4 oxrna2/hbond   seqdep oxrna2_real.cgdna
pair_coeff * * oxrna2/xstk    oxrna2_real.cgdna
pair_coeff * * oxrna2/coaxstk oxrna2_real.cgdna
pair_coeff * * oxrna2/dh      300.0 0.5 oxrna2_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 oxrna2 pair styles compute the pairwise-additive parts of the oxDNA force field for coarse-grained modelling of RNA. The effective interaction between the nucleotides consists of potentials for the excluded volume interaction oxrna2/excv, the stacking oxrna2/stk, cross-stacking oxrna2/xstk and coaxial stacking interaction oxrna2/coaxstk, electrostatic Debye-Hueckel interaction oxrna2/dh as well as the hydrogen-bonding interaction oxrna2/hbond between complementary pairs of nucleotides on opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths are supported (Sulc2).

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 (Sulc1) and the original oxDNA publications (Ouldridge-DPhil) and (Ouldridge) for a detailed description of the oxRNA2 force field.

Note

These pair styles have to be used together with the related oxDNA2 bond style oxrna2/fene for the connectivity of the phosphate backbone (see also documentation of bond_style oxrna2/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 oxrna2/stk (seq=seqdep and T=0.1 and corresponding real unit equivalents in the above examples), the first coefficient after oxrna2/hbond (seq=seqdep in the above example) and the two coefficients after oxrna2/dh (T=0.1 and rhos=0.5 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/oxRNA2/ 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. The article contains general information on the model, its implementation and performance as well as the structure of the data and input file. The preprint version of the article can be found here. Please cite also the relevant oxRNA2 publications (Sulc1) and (Sulc2).

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 3 4 oxrna2/hbond   seqdep oxrna2_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:

3 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 oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
pair_coeff * * oxrna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxrna2/stk     seqdep 0.1 oxrna2_lj.cgdna
pair_coeff * * oxrna2/hbond   seqdep oxrna2_lj.cgdna
pair_coeff 1 4 oxrna2/hbond   seqdep oxrna2_lj.cgdna
pair_coeff 2 3 oxrna2/hbond   seqdep oxrna2_lj.cgdna
pair_coeff 3 4 oxrna2/hbond   seqdep oxrna2_lj.cgdna
pair_coeff * * oxrna2/xstk    oxrna2_lj.cgdna
pair_coeff * * oxrna2/coaxstk oxrna2_lj.cgdna
pair_coeff * * oxrna2/dh      0.1 0.5 1.02455

will read the excluded volume and Debye-Hueckel effective charge qeff parameters from the manual specification and all others from the potential file oxrna2_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).

(Sulc1) P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).

(Sulc2) 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).