dihedral_style charmm command — LAMMPS documentation

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# dihedral_style charmm command

Accelerator Variants: charmm/intel, charmm/kk, charmm/omp

# dihedral_style charmmfsw command

## Syntax

    dihedral_style style

- style = charmm or charmmfsw

## Examples

    dihedral_style charmm
    dihedral_style charmmfsw
    dihedral_coeff  1 0.2 1 180 1.0
    dihedral_coeff  2 1.8 1   0 1.0
    dihedral_coeff  1 3.1 2 180 0.5

## Description

The charmm and charmmfsw dihedral styles use the potential

\[E = K [ 1 + \cos (n \phi - d) ]\]

See (MacKerell) for a description of the CHARMM force field. This dihedral style can also be used for the AMBER force field (see comment on weighting factors below). See (Cornell) for a description of the AMBER force field.

Note

The newer charmmfsw style was released in March 2017. We recommend it be used instead of the older charmm style when running a simulation with the CHARMM force field, either with long-range Coulombics or a Coulombic cutoff, via the pair_style lj/charmmfsw/coul/long and pair_style lj/charmmfsw/coul/charmmfsh commands respectively. Otherwise the older charmm style is fine to use. See the discussion below and more details on the pair_style charmm doc page.

The following coefficients must be defined for each dihedral type via the dihedral_coeff command as in the example above, or in the data file or restart files read by the read_data or read_restart commands:

- \(K\) (energy)

- \(n\) (integer >= 0)

- \(d\) (integer value of degrees)

- weighting factor (1.0, 0.5, or 0.0)

The weighting factor is required to correct for double counting pairwise non-bonded Lennard-Jones interactions in cyclic systems or when using the CHARMM dihedral style with non-CHARMM force fields. With the CHARMM dihedral style, interactions between the first and fourth atoms in a dihedral are skipped during the normal non-bonded force computation and instead evaluated as part of the dihedral using special epsilon and sigma values specified with the pair_coeff command of pair styles that contain “lj/charmm” (e.g. pair_style lj/charmm/coul/long) In 6-membered rings, the same 1-4 interaction would be computed twice (once for the clockwise 1-4 pair in dihedral 1-2-3-4 and once in the counterclockwise dihedral 1-6-5-4) and thus the weighting factor has to be 0.5 in this case. In 4-membered or 5-membered rings, the 1-4 dihedral also is counted as a 1-2 or 1-3 interaction when going around the ring in the opposite direction and thus the weighting factor is 0.0, as the 1-2 and 1-3 exclusions take precedence.

Note that this dihedral weighting factor is unrelated to the scaling factor specified by the special bonds command which applies to all 1-4 interactions in the system. For CHARMM force fields, the special_bonds 1-4 interaction scaling factor should be set to 0.0. Since the corresponding 1-4 non-bonded interactions are computed with the dihedral. This means that if any of the weighting factors defined as dihedral coefficients (fourth coeff above) are non-zero, then you must use a pair style with “lj/charmm” and set the special_bonds 1-4 scaling factor to 0.0 (which is the default). Otherwise 1-4 non-bonded interactions in dihedrals will be computed twice.

For simulations using the CHARMM force field with a Coulombic cutoff, the difference between the charmm and charmmfsw styles is in the computation of the 1-4 non-bond interactions, though only if the distance between the two atoms is within the switching region of the pairwise potential defined by the corresponding CHARMM pair style, i.e. within the outer cutoff specified for the pair style. The charmmfsw style should only be used when using the corresponding pair_style lj/charmmfsw/coul/charmmfsw or pair_style lj/charmmfsw/coul/long commands. Use the charmm style with the older pair_style commands that have just “charmm” in their style name. See the discussion on the CHARMM pair_style page for details.

Note that for AMBER force fields, which use pair styles with “lj/cut”, the special_bonds 1-4 scaling factor should be set to the AMBER defaults (1/2 and 5/6) and all the dihedral weighting factors (fourth coeff above) must be set to 0.0. In this case, you can use any pair style you wish, since the dihedral does not need any Lennard-Jones parameter information and will not compute any 1-4 non-bonded interactions. Likewise the charmm or charmmfsw styles are identical in this case since no 1-4 non-bonded interactions are computed.

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.

## Restrictions

When using run_style respa, these dihedral styles must be assigned to the same r-RESPA level as pair or outer.

When used in combination with CHARMM pair styles, the 1-4 special_bonds scaling factors must be set to 0.0. Otherwise non-bonded contributions for these 1-4 pairs will be computed multiple times.

These dihedral styles can only be used if LAMMPS was built with the MOLECULE package. See the Build package doc page for more info.

## Related commands

dihedral_coeff

## Default

none

(Cornell) Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).

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