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pair_style 3spn2 command

Syntax:

pair_style 3spn2 T salt Rc

Examples:

Description:

Style 3spn2 computes interactions based on the non-bonded potentials from (Hinckley) for the simulation of coarse-grained DNA. Style 3spn2 includes all non-bonded components from (Hinckley) besides base stacking which is currently implemented in angle_3spn2_stacking.

This pair style is not a true pair style, as it calcules angle-dependent potentials that are functions of the positions of up to 6 atoms. The contributions to the non-bonded energy function shown above are as follows.

The excluded volume energy is

where epsilon and sigma are obtained using arithmetic mixing rules with the values provided with the pair_coeff command.

The base pairing and cross stacking energies are

and

with the values of the epsilon's, alpha's, and K's being specific to the type of each atom and hard-coded into pair_3spn.cpp.

As in angle_3spn2_stacking the Morse potential Em is decomposed into repulsive

and attractive components

The attractive portion of the potential is modulated by the function f

which uses the difference between the instantenous angle and reference angle (Delta theta = theta - theta_o) and a factor K. The differences in angle shown above (Delta theta[1-3] and Delta phi) refer to deviations from reference angles extracted from the crystal structure of B-DNA. Each epsilon is unique to the identity of the atoms involved, as is the equilibrium difference r0. These values are hard-coded into the pair style. The user is referred to (Hinckley) for additional details on how these parameters are assigned.

Lastly, electrostatic interactions are calculated at the level of Debye-Huckel, as in pair style coul/debye as described in pair_coul.

This potential has the same form as pair style coul/debye and includes C as the energy-conversion constant, the inverse Debye length Kappa and the charges Qi and Qj. Noticeable differences include the temperature and ionic strength-dependent dielectric constant and. See (Hinckley) for the functional dependence on these variables. Because the dielectric constant is calculated with the pair style, using the dielectric command will have no effect.

The compute_pair command should be used to calculate the energy of the different contributions to the pair style. The calculated quantities are returned as a vector, organized as follows: [Ebp Ecstk Eexe Ecoul Nbp]. The last value is the number of base pairs being formed.

The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples above, or in the data file or restart files read by the read_data or read_restart commands.

These units are used in the calculation of excluded volume interactions. Other parameters used in the non-bonded interactions are hard-coded into the 3spn2 pair style source code.

NOTE: It is not recommended that the short-range cutoff be changed.


Mixing, shift, table, tail correction, restart, rRESPA info:

For atom type pairs I,J and I != J, arithmetic mixing rules MUST be used.

This pair style does not support the pair_modify shift, table and tail options.

This pair style writes its information to binary restart files, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file.

This pair style can only be used via the pair keyword of the run_style respa command. It does not support the inner, middle, outer keywords.


Restrictions:

This pair style is part of the USER-3SPN2 package. It is only enabled if LAMMPS was build with that package. See the Making_LAMMPS section for more info.

The hard-coded values of the reference distances Ro and epsilon are currently in Angstroms and kcal/mol, respectively. In addition, tthe temperature and ionic strength specified as pair_style arguments are to be specified in Kelvin and milliMolar (mM). Therefore, real units should be used.

Related commands:

pair_coeff

Default: none


(Hinckley) Hinckley, Freeman, Whitmer and de Pablo. J Chem Phys, 139, 144903 (2013).