\(\renewcommand{\AA}{\text{Å}}\)
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 1.40206 2.77 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 8.35864576375849 0.005504556 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). 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 (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 four coefficients after oxrna2/stk (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 and corresponding real unit equivalents in the above examples), the first coefficient after oxrna2/hbond (seq=seqdep in the above example) and the three coefficients after oxrna2/dh (T=0.1, rhos=0.5, qeff=1.02455 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. 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 1.40206 2.77 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/
.
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).