pair_style lj/charmm/coul/charmm command — LAMMPS documentation

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# pair_style lj/charmm/coul/charmm command

Accelerator Variants: lj/charmm/coul/charmm/gpu, lj/charmm/coul/charmm/intel, lj/charmm/coul/charmm/kk, lj/charmm/coul/charmm/omp

# pair_style lj/charmm/coul/charmm/implicit command

Accelerator Variants: lj/charmm/coul/charmm/implicit/kk, lj/charmm/coul/charmm/implicit/omp

# pair_style lj/charmm/coul/long command

Accelerator Variants: lj/charmm/coul/long/gpu, lj/charmm/coul/long/intel, lj/charmm/coul/long/kk, lj/charmm/coul/long/opt, lj/charmm/coul/long/omp

# pair_style lj/charmm/coul/msm command

Accelerator Variants: lj/charmm/coul/msm/omp

# pair_style lj/charmmfsw/coul/charmmfsh command

# pair_style lj/charmmfsw/coul/long command

## Syntax

    pair_style style args

- style = lj/charmm/coul/charmm or lj/charmm/coul/charmm/implicit or lj/charmm/coul/long or lj/charmm/coul/msm or lj/charmmfsw/coul/charmmfsh or lj/charmmfsw/coul/long

- args = list of arguments for a particular style

    lj/charmm/coul/charmm args = inner outer (inner2) (outer2)
      inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
      inner2, outer2 = global switching cutoffs for Coulombic (optional)
    lj/charmm/coul/charmm/implicit args = inner outer (inner2) (outer2)
      inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
      inner2, outer2 = global switching cutoffs for Coulombic (optional)
    lj/charmm/coul/long args = inner outer (cutoff)
      inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
      cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
    lj/charmm/coul/msm args = inner outer (cutoff)
      inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
      cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
    lj/charmmfsw/coul/charmmfsh args = inner outer (cutoff)
      inner, outer = global cutoffs for LJ (and Coulombic if only 2 args)
      cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
    lj/charmmfsw/coul/long args = inner outer (cutoff)
      inner, outer = global cutoffs for LJ (and Coulombic if only 2 args)
      cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)

## Examples

    pair_style lj/charmm/coul/charmm 8.0 10.0
    pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
    pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0
    pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0 9.0
    pair_coeff * * 100.0 2.0
    pair_coeff 1 1 100.0 2.0 150.0 3.5

    pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
    pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
    pair_coeff * * 100.0 2.0
    pair_coeff 1 1 100.0 2.0 150.0 3.5

    pair_style lj/charmm/coul/long 8.0 10.0
    pair_style lj/charmm/coul/long 8.0 10.0 9.0
    pair_style lj/charmmfsw/coul/long 8.0 10.0
    pair_style lj/charmmfsw/coul/long 8.0 10.0 9.0
    pair_coeff * * 100.0 2.0
    pair_coeff 1 1 100.0 2.0 150.0 3.5

    pair_style lj/charmm/coul/msm 8.0 10.0
    pair_style lj/charmm/coul/msm 8.0 10.0 9.0
    pair_coeff * * 100.0 2.0
    pair_coeff 1 1 100.0 2.0 150.0 3.5

## Description

These pair styles compute Lennard Jones (LJ) and Coulombic interactions with additional switching or shifting functions that ramp the energy and/or force smoothly to zero between an inner and outer cutoff. They are implementations of the widely used CHARMM force field used in the CHARMM MD code (and others). See (MacKerell) for a description of the CHARMM force field.

The styles with charmm (not charmmfsw or charmmfsh) in their name are the older, original LAMMPS implementations. They compute the LJ and Coulombic interactions with an energy switching function (esw, shown in the formula below as S(r)), which ramps the energy smoothly to zero between the inner and outer cutoff. This can cause irregularities in pairwise forces (due to the discontinuous second derivative of energy at the boundaries of the switching region), which in some cases can result in detectable artifacts in an MD simulation.

The newer styles with charmmfsw or charmmfsh in their name replace the energy switching with force switching (fsw) and force shifting (fsh) functions, for LJ and Coulombic interactions respectively. These follow the formulas and description given in (Steinbach) and (Brooks) to minimize these artifacts.

Note

The newer charmmfsw or charmmfsh styles were released in March 2017. We recommend they be used instead of the older charmm styles. This includes the newer dihedral_style charmmfsw command. Eventually code from the new styles will propagate into the related pair styles (e.g. implicit, accelerator, free energy variants).

Note

The newest CHARMM pair styles reset the Coulombic energy conversion factor used internally in the code, from the LAMMPS value to the CHARMM value, as if it were effectively a parameter of the force field. This is because the CHARMM code uses a slightly different value for the this conversion factor in real units (kcal/mol), namely CHARMM = 332.0716, LAMMPS = 332.06371. This is to enable more precise agreement by LAMMPS with the CHARMM force field energies and forces, when using one of these two CHARMM pair styles.

\[\begin{split}E = & LJ(r) \qquad \qquad \qquad r < r_{\rm in} \\ = & S(r) * LJ(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\ E = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\ = & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\ LJ(r) = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \\ C(r) = & \frac{C q_i q_j}{ \epsilon r} \\ S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2 \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]} { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }\end{split}\]

where S(r) is the energy switching function mentioned above for the charmm styles. See the (Steinbach) paper for the functional forms of the force switching and force shifting functions used in the charmmfsw and charmmfsh styles.

When using the lj/charmm/coul/charmm styles, both the LJ and Coulombic terms require an inner and outer cutoff. They can be the same for both formulas or different depending on whether 2 or 4 arguments are used in the pair_style command. For the lj/charmmfsw/coul/charmmfsh style, the LJ term requires both an inner and outer cutoff, while the Coulombic term requires only one cutoff. If the Coulombic cutoff is not specified (2 instead of 3 arguments), the LJ outer cutoff is used for the Coulombic cutoff. In all cases where an inner and outer cutoff are specified, the inner cutoff distance must be less than the outer cutoff. It is typical to make the difference between the inner and outer cutoffs about 2.0 Angstroms.

Style lj/charmm/coul/charmm/implicit computes the same formulas as style lj/charmm/coul/charmm except that an additional 1/r term is included in the Coulombic formula. The Coulombic energy thus varies as 1/r^2. This is effectively a distance-dependent dielectric term which is a simple model for an implicit solvent with additional screening. It is designed for use in a simulation of an unsolvated biomolecule (no explicit water molecules).

Styles lj/charmm/coul/long and lj/charmm/coul/msm compute the same formulas as style lj/charmm/coul/charmm and style lj/charmmfsw/coul/long computes the same formulas as style lj/charmmfsw/coul/charmmfsh, except that an additional damping factor is applied to the Coulombic term, so it can be used in conjunction with the kspace_style command and its ewald or pppm or msm option. Only one Coulombic cutoff is specified for these styles; if only 2 arguments are used in the pair_style command, then the outer LJ cutoff is used as the single Coulombic cutoff. The Coulombic cutoff specified for these styles means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space.

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, or by mixing as described below:

- \(\epsilon\) (energy units)

- \(\sigma\) (distance units)

- \(\epsilon_{14}\) (energy units)

- \(\sigma_{14}\) (distance units)

Note that \(\sigma\) is defined in the LJ formula as the zero-crossing distance for the potential, not as the energy minimum at \(2^{1/6} \sigma\).

The latter 2 coefficients are optional. If they are specified, they are used in the LJ formula between 2 atoms of these types which are also first and fourth atoms in any dihedral. No cutoffs are specified because the CHARMM force field does not allow varying cutoffs for individual atom pairs; all pairs use the global cutoff(s) specified in the pair_style command.

Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the Accelerator packages page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

These accelerated styles are part of the GPU, INTEL, KOKKOS, OPENMP, and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the Build package page for more info.

You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

See the Accelerator packages page for more instructions on how to use the accelerated styles effectively.

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

For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14, and sigma_14 coefficients for all of the lj/charmm pair styles can be mixed. The default mix value is arithmetic to coincide with the usual settings for the CHARMM force field. See the “pair_modify” command for details.

None of the lj/charmm or lj/charmmfsw pair styles support the pair_modify shift option, since the Lennard-Jones portion of the pair interaction is smoothed to 0.0 at the cutoff.

The lj/charmm/coul/long and lj/charmmfsw/coul/long styles support the pair_modify table option since they can tabulate the short-range portion of the long-range Coulombic interaction.

None of the lj/charmm or lj/charmmfsw pair styles support the pair_modify tail option for adding long-range tail corrections to energy and pressure, since the Lennard-Jones portion of the pair interaction is smoothed to 0.0 at the cutoff.

All of the lj/charmm and lj/charmmfsw pair styles write their 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.

The lj/charmm/coul/long and lj/charmmfsw/coul/long pair styles support the use of the inner, middle, and outer keywords of the run_style respa command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. The other styles only support the pair keyword of run_style respa. See the run_style command for details.

## Restrictions

All the styles with coul/charmm or coul/charmmfsh styles are part of the MOLECULE package. All the styles with coul/long style are part of the KSPACE package. They are only enabled if LAMMPS was built with those packages. See the Build package doc page for more info.

## Related commands

pair_coeff

## Default

none

(Brooks) Brooks, et al, J Comput Chem, 30, 1545 (2009).

(MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).

(Steinbach) Steinbach, Brooks, J Comput Chem, 15, 667 (1994).