forked from lijiext/lammps
272 lines
12 KiB
Plaintext
272 lines
12 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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pair_style lj/charmm/coul/charmm command :h3
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pair_style lj/charmm/coul/charmm/intel command :h3
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pair_style lj/charmm/coul/charmm/kk command :h3
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pair_style lj/charmm/coul/charmm/omp command :h3
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pair_style lj/charmm/coul/charmm/implicit command :h3
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pair_style lj/charmm/coul/charmm/implicit/kk command :h3
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pair_style lj/charmm/coul/charmm/implicit/omp command :h3
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pair_style lj/charmm/coul/long command :h3
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pair_style lj/charmm/coul/long/gpu command :h3
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pair_style lj/charmm/coul/long/intel command :h3
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pair_style lj/charmm/coul/long/kk command :h3
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pair_style lj/charmm/coul/long/opt command :h3
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pair_style lj/charmm/coul/long/omp command :h3
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pair_style lj/charmm/coul/msm command :h3
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pair_style lj/charmm/coul/msm/omp command :h3
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pair_style lj/charmmfsw/coul/charmmfsh command :h3
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pair_style lj/charmmfsw/coul/long command :h3
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[Syntax:]
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pair_style style args :pre
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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}
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args = list of arguments for a particular style :ul
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{lj/charmm/coul/charmm} args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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{lj/charmm/coul/charmm/implicit} args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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{lj/charmm/coul/long} args = inner outer (cutoff)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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{lj/charmm/coul/msm} args = inner outer (cutoff)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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{lj/charmmfsw/coul/charmmfsh} args = inner outer (cutoff)
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inner, outer = global cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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{lj/charmmfsw/coul/long} args = inner outer (cutoff)
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inner, outer = global cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) :pre
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[Examples:]
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pair_style lj/charmm/coul/charmm 8.0 10.0
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pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
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pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0
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pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
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pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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pair_style lj/charmm/coul/long 8.0 10.0
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pair_style lj/charmm/coul/long 8.0 10.0 9.0
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pair_style lj/charmmfsw/coul/long 8.0 10.0
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pair_style lj/charmmfsw/coul/long 8.0 10.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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pair_style lj/charmm/coul/msm 8.0 10.0
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pair_style lj/charmm/coul/msm 8.0 10.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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[Description:]
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These pair styles compute Lennard Jones (LJ) and Coulombic
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interactions with additional switching or shifting functions that ramp
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the energy and/or force smoothly to zero between an inner and outer
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cutoff. They are implementations of the widely used CHARMM force
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field used in the "CHARMM"_http://www.scripps.edu/brooks MD code (and
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others). See "(MacKerell)"_#pair-MacKerell for a description of the
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CHARMM force field.
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The styles with {charmm} (not {charmmfsw} or {charmmfsh}) in their
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name are the older, original LAMMPS implementations. They compute the
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LJ and Coulombic interactions with an energy switching function (esw,
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shown in the formula below as S(r)), which ramps the energy smoothly
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to zero between the inner and outer cutoff. This can cause
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irregularities in pair-wise forces (due to the discontinuous 2nd
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derivative of energy at the boundaries of the switching region), which
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in some cases can result in detectable artifacts in an MD simulation.
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The newer styles with {charmmfsw} or {charmmfsh} in their name replace
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the energy switching with force switching (fsw) and force shifting
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(fsh) functions, for LJ and Coulombic interactions respectively.
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These follow the formulas and description given in
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"(Steinbach)"_#Steinbach and "(Brooks)"_#Brooks1 to minimize these
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artifacts.
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NOTE: The newer {charmmfsw} or {charmmfsh} styles were released in
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March 2017. We recommend they be used instead of the older {charmm}
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styles. This includes the newer "dihedral_style
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charmmfsw"_dihedral_charmm.html command. Eventually code from the new
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styles will propagate into the related pair styles (e.g. implicit,
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accelerator, free energy variants).
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NOTE: The newest CHARMM pair styles reset the Coulombic energy
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conversion factor used internally in the code, from the LAMMPS value
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to the CHARMM value, as if it were effectively a parameter of the
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force field. This is because the CHARMM code uses a slightly
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different value for the this conversion factor in "real
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units"_units.html (Kcal/mole), namely CHARMM = 332.0716, LAMMPS =
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332.06371. This is to enable more precise agreement by LAMMPS with
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the CHARMM force field energies and forces, when using one of these
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two CHARMM pair styles.
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:c,image(Eqs/pair_charmm.jpg)
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where S(r) is the energy switching function mentioned above for the
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{charmm} styles. See the "(Steinbach)"_#Steinbach paper for the
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functional forms of the force switching and force shifting functions
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used in the {charmmfsw} and {charmmfsh} styles.
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When using the {lj/charmm/coul/charmm styles}, both the LJ and
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Coulombic terms require an inner and outer cutoff. They can be the
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same for both formulas or different depending on whether 2 or 4
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arguments are used in the pair_style command. For the
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{lj/charmmfsw/coul/charmmfsh} style, the LJ term requires both an
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inner and outer cutoff, while the Coulombic term requires only one
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cutoff. If the Coulombic cutoff is not specified (2 instead of 3
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arguments), the LJ outer cutoff is used for the Coulombic cutoff. In
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all cases where an inner and outer cutoff are specified, the inner
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cutoff distance must be less than the outer cutoff. It is typical to
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make the difference between the inner and outer cutoffs about 2.0
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Angstroms.
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Style {lj/charmm/coul/charmm/implicit} computes the same formulas as
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style {lj/charmm/coul/charmm} except that an additional 1/r term is
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included in the Coulombic formula. The Coulombic energy thus varies
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as 1/r^2. This is effectively a distance-dependent dielectric term
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which is a simple model for an implicit solvent with additional
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screening. It is designed for use in a simulation of an unsolvated
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biomolecule (no explicit water molecules).
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Styles {lj/charmm/coul/long} and {lj/charmm/coul/msm} compute the same
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formulas as style {lj/charmm/coul/charmm} and style
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{lj/charmmfsw/coul/long} computes the same formulas as style
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{lj/charmmfsw/coul/charmmfsh}, except that an additional damping
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factor is applied to the Coulombic term, so it can be used in
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conjunction with the "kspace_style"_kspace_style.html command and its
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{ewald} or {pppm} or {msm} option. Only one Coulombic cutoff is
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specified for these styles; if only 2 arguments are used in the
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pair_style command, then the outer LJ cutoff is used as the single
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Coulombic cutoff. The Coulombic cutoff specified for these styles
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means that pairwise interactions within this distance are computed
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directly; interactions outside that distance are computed in
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reciprocal space.
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The following coefficients must be defined for each pair of atoms
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types via the "pair_coeff"_pair_coeff.html command as in the examples
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above, or in the data file or restart files read by the
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands, or by mixing as described below:
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epsilon (energy units)
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sigma (distance units)
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epsilon_14 (energy units)
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sigma_14 (distance units) :ul
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Note that sigma is defined in the LJ formula as the zero-crossing
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distance for the potential, not as the energy minimum at 2^(1/6)
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sigma.
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The latter 2 coefficients are optional. If they are specified, they
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are used in the LJ formula between 2 atoms of these types which are
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also first and fourth atoms in any dihedral. No cutoffs are specified
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because the CHARMM force field does not allow varying cutoffs for
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individual atom pairs; all pairs use the global cutoff(s) specified in
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the pair_style command.
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:line
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Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed on the "Speed packages"_Speed_packages.html doc
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page. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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LAMMPS was built with those packages. See the "Build
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package"_Build_package.html doc page for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the "-suffix command-line
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switch"_Run_options.html when you invoke LAMMPS, or you can use the
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"suffix"_suffix.html command in your input script.
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See the "Speed packages"_Speed_packages.html doc page for more
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instructions on how to use the accelerated styles effectively.
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:line
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
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and sigma_14 coefficients for all of the lj/charmm pair styles can be
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mixed. The default mix value is {arithmetic} to coincide with the
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usual settings for the CHARMM force field. See the "pair_modify"
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command for details.
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None of the {lj/charmm} or {lj/charmmfsw} pair styles support the
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"pair_modify"_pair_modify.html shift option, since the Lennard-Jones
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portion of the pair interaction is smoothed to 0.0 at the cutoff.
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The {lj/charmm/coul/long} and {lj/charmmfsw/coul/long} styles support
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the "pair_modify"_pair_modify.html table option since they can
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tabulate the short-range portion of the long-range Coulombic
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interaction.
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None of the {lj/charmm} or {lj/charmmfsw} pair styles support the
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"pair_modify"_pair_modify.html tail option for adding long-range tail
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corrections to energy and pressure, since the Lennard-Jones portion of
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the pair interaction is smoothed to 0.0 at the cutoff.
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All of the {lj/charmm} and {lj/charmmfsw} pair styles write their
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information to "binary restart files"_restart.html, so pair_style and
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pair_coeff commands do not need to be specified in an input script
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that reads a restart file.
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The {lj/charmm/coul/long} and {lj/charmmfsw/coul/long} pair styles
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support the use of the {inner}, {middle}, and {outer} keywords of the
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"run_style respa"_run_style.html command, meaning the pairwise forces
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can be partitioned by distance at different levels of the rRESPA
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hierarchy. The other styles only support the {pair} keyword of
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run_style respa. See the "run_style"_run_style.html command for
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details.
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:line
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[Restrictions:]
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All the styles with {coul/charmm} or {coul/charmmfsh} styles are part
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of the MOLECULE package. All the styles with {coul/long} style are
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part of the KSPACE package. They are only enabled if LAMMPS was built
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with those packages. See the "Build package"_Build_package.html doc
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page for more info.
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[Related commands:]
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"pair_coeff"_pair_coeff.html
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[Default:] none
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:line
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:link(Brooks1)
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[(Brooks)] Brooks, et al, J Comput Chem, 30, 1545 (2009).
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:link(pair-MacKerell)
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[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
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Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
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:link(Steinbach)
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[(Steinbach)] Steinbach, Brooks, J Comput Chem, 15, 667 (1994).
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