forked from lijiext/lammps
171 lines
6.9 KiB
Plaintext
171 lines
6.9 KiB
Plaintext
"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/implicit command :h3
|
|
pair_style lj/charmm/coul/long command :h3
|
|
pair_style lj/charmm/coul/long/opt 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/long/opt}
|
|
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) :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_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/opt 8.0 10.0
|
|
pair_style lj/charmm/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
|
|
|
|
[Description:]
|
|
|
|
The {lj/charmm} styles compute LJ and Coulombic interactions with an
|
|
additional switching function S(r) that ramps the energy and force
|
|
smoothly to zero between an inner and outer cutoff. It is a widely
|
|
used potential in the "CHARMM"_http://www.scripps.edu/brooks MD code.
|
|
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
|
|
field.
|
|
|
|
:c,image(Eqs/pair_charmm.jpg)
|
|
|
|
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. In each
|
|
case, the inner cutoff distance must be less than the outer cutoff.
|
|
It it typical to make the difference between the 2 cutoffs about 1.0
|
|
Angstrom.
|
|
|
|
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).
|
|
|
|
Style {lj/charmm/coul/long} computes the same formulas as style
|
|
{lj/charmm/coul/charmm} except that an additional damping factor is
|
|
applied to the Coulombic term, as in the discussion for pair style
|
|
{lj/cut/coul/long}. Only one Coulombic cutoff is specified for
|
|
{lj/charmm/coul/long}; if only 2 arguments are used in the pair_style
|
|
command, then the outer LJ cutoff is used as the single Coulombic
|
|
cutoff.
|
|
|
|
Style {lj/charmm/coul/long/opt} is an optimized version of style
|
|
{lj/charmm/coul/long} that should give identical answers. Depending
|
|
on system size and the processor you are running on, it may be 5-25%
|
|
faster (for the pairwise portion of the run time).
|
|
|
|
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 this 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
|
|
|
|
[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. They are always mixed with the value {arithmetic}. See the
|
|
"pair_modify" command for details.
|
|
|
|
None of the lj/charmm 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/charmm/coul/long/opt} pair 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 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 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 pair style supports 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:]
|
|
|
|
The {lj/charmm/coul/charmm} and {lj/charmm/coul/charmm/implicit}
|
|
styles are part of the "molecule" package. The {lj/charmm/coul/long}
|
|
style is part of the "kspace" package. The {lj/charmm/coul/long/opt}
|
|
style is part of the "opt" package and also requires the "kspace"
|
|
package. They are only enabled if LAMMPS was built with those
|
|
package(s) (molecule and kspace are by default). See the "Making
|
|
LAMMPS"_Section_start.html#2_3 section for more info.
|
|
|
|
On some 64-bit machines, compiling with -O3 appears to break the
|
|
Coulombic tabling option used by the {lj/charmm/coul/long} style. See
|
|
the "Additional build tips" section of the Making LAMMPS documentation
|
|
pages for workarounds on this issue.
|
|
|
|
[Related commands:]
|
|
|
|
"pair_coeff"_pair_coeff.html
|
|
|
|
[Default:] none
|
|
|
|
:line
|
|
|
|
:link(MacKerell)
|
|
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
|
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
|