dihedral_style charmm command

dihedral_style charmm/intel command

dihedral_style charmm/kk command

dihedral_style charmm/omp command

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

_images/dihedral_charmm.jpg

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 Coulomb 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 1st and 4th 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 (4th 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 Coulomb 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 doc 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 (4th 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 in Section 5 of the manual. 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, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the Making LAMMPS section 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 Section 5 of the manual for more instructions on how to use the accelerated styles effectively.


Restrictions

This dihedral style can only be used if LAMMPS was built with the MOLECULE package. See the Making LAMMPS section for more info on packages.