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lammps/doc/src/dihedral_charmm.txt
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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
dihedral_style charmm command :h3
dihedral_style charmm/intel command :h3
dihedral_style charmm/kk command :h3
dihedral_style charmm/omp command :h3
[Syntax:]
dihedral_style charmm :pre
[Examples:]
dihedral_style charmm
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 :pre
[Description:]
The {charmm} dihedral style uses the potential
:c,image(Eqs/dihedral_charmm.jpg)
See "(MacKerell)"_#dihedral-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)"_#dihedral-Cornell for a description of the AMBER force
field.
The following coefficients must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy)
n (integer >= 0)
d (integer value of degrees)
weighting factor (1.0, 0.5, or 0.0) :ul
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"_pair_charmm.html command of pair styles that contain
"lj/charmm" (e.g. "pair_style lj/charmm/coul/long"_pair_charmm.html)
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"_special_bonds.html 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.
Also 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.
: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_accelerate"_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_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:] none
:line
:link(dihedral-Cornell)
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
:link(dihedral-MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).
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