forked from lijiext/lammps
115 lines
4.2 KiB
Plaintext
115 lines
4.2 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
|
|
|
|
dihedral_style charmm 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 1 120.0 1 60 0.5 :pre
|
|
|
|
[Description:]
|
|
|
|
The {charmm} dihedral style uses the potential
|
|
|
|
:c,image(Eqs/dihedral_charmm.jpg)
|
|
|
|
See "(MacKerell)"_#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)"_#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 (0.0 to 1.0) :ul
|
|
|
|
The weighting factor is applied to pairwise interaction between the
|
|
1st and 4th atoms in the dihedral, which are computed by a CHARMM
|
|
"pair_style"_pair_charmm.html with epsilon and sigma values specified
|
|
with a "pair_coeff"_pair_charmm.html command. Note that this
|
|
weighting factor is unrelated to the weighting 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 weighting factor should
|
|
be set to 0.0. This is because the pair styles that contain "charmm"
|
|
(e.g. "pair_style lj/charmm/coul/long"_pair_charmm.html) define extra
|
|
1-4 interaction coefficients that are used by this dihedral style to
|
|
compute those interactions explicitly. This means that if any of the
|
|
weighting factors defined as dihedral coefficients (4th coeff above)
|
|
are non-zero, then you must use a charmm pair style. Note that if you
|
|
do not set the special_bonds 1-4 weighting factor to 0.0 (which is the
|
|
default) then 1-4 interactions in dihedrals will be computed twice,
|
|
once by the pair routine and once by the dihedral routine, which is
|
|
probably not what you want.
|
|
|
|
For AMBER force fields, the special_bonds 1-4 weighting factor should
|
|
be set to the AMBER defaults (1/2 and 5/6) and all the dihedral
|
|
weighting factors (4th coeff above) should be set to 0.0. In this
|
|
case, you can use any pair style you wish, since the dihedral does not
|
|
need any 1-4 information.
|
|
|
|
:line
|
|
|
|
Styles with a {cuda}, {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 USER-CUDA, 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(Cornell)
|
|
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
|
|
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
|
|
|
|
:link(MacKerell)
|
|
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
|
Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).
|