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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lj/charmm/coul/charmm command :h3
pair_style lj/charmm/coul/charmm/omp command :h3
pair_style lj/charmm/coul/charmm/implicit command :h3
pair_style lj/charmm/coul/charmm/implicit/omp command :h3
pair_style lj/charmm/coul/long command :h3
pair_style lj/charmm/coul/long/gpu command :h3
pair_style lj/charmm/coul/long/intel command :h3
pair_style lj/charmm/coul/long/opt command :h3
pair_style lj/charmm/coul/long/omp command :h3
pair_style lj/charmm/coul/msm command :h3
pair_style lj/charmm/coul/msm/omp command :h3
pair_style lj/charmmfsw/coul/charmmfsh command :h3
pair_style lj/charmmfsw/coul/long command :h3
[Syntax:]
pair_style style args :pre
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 :ul
{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) :pre
[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 :pre
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 :pre
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 :pre
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 :pre
[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"_http://www.scripps.edu/brooks MD code (and
others). See "(MacKerell)"_#pair-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 pair-wise forces (due to the discontinuous 2nd
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)"_#Steinbach and "(Brooks)"_#Brooks1 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"_dihedral_charmm.html 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"_units.html (Kcal/mole), 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.
:c,image(Eqs/pair_charmm.jpg)
where S(r) is the energy switching function mentioned above for the
{charmm} styles. See the "(Steinbach)"_#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 Coulomb 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"_kspace_style.html 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"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
epsilon_14 (energy units)
sigma_14 (distance units) :ul
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.
:line
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"_Section_accelerate.html
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_start.html#start_3 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"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[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"_pair_modify.html 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"_pair_modify.html 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"_pair_modify.html 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"_restart.html, 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"_run_style.html 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"_run_style.html command for
details.
:line
[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 "Making
LAMMPS"_Section_start.html#start_3 section for more info. Note that
the MOLECULE and KSPACE packages are installed by default.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Brooks1)
[(Brooks)] Brooks, et al, J Comput Chem, 30, 1545 (2009).
:link(pair-MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
:link(Steinbach)
[(Steinbach)] Steinbach, Brooks, J Comput Chem, 15, 667 (1994).
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