forked from lijiext/lammps
167 lines
6.8 KiB
Plaintext
167 lines
6.8 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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dihedral_style charmm command :h3
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dihedral_style charmm/intel command :h3
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dihedral_style charmm/kk command :h3
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dihedral_style charmm/omp command :h3
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dihedral_style charmmfsw command :h3
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[Syntax:]
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dihedral_style style :pre
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style = {charmm} or {charmmfsw} :ul
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[Examples:]
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dihedral_style charmm
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dihedral_style charmmfsw
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dihedral_coeff 1 0.2 1 180 1.0
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dihedral_coeff 2 1.8 1 0 1.0
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dihedral_coeff 1 3.1 2 180 0.5 :pre
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[Description:]
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The {charmm} and {charmmfsw} dihedral styles use the potential
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:c,image(Eqs/dihedral_charmm.jpg)
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See "(MacKerell)"_#dihedral-MacKerell for a description of the CHARMM
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force field. This dihedral style can also be used for the AMBER force
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field (see comment on weighting factors below). See
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"(Cornell)"_#dihedral-Cornell for a description of the AMBER force
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field.
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NOTE: The newer {charmmfsw} style was released in March 2017. We
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recommend it be used instead of the older {charmm} style when running
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a simulation with the CHARMM force field, either with long-range
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Coulombics or a Coulombic cutoff, via the "pair_style
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lj/charmmfsw/coul/long"_pair_charmm.html and "pair_style
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lj/charmmfsw/coul/charmmfsh"_pair_charmm.html commands respectively.
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Otherwise the older {charmm} style is fine to use. See the discussion
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below and more details on the "pair_style charmm"_pair_charmm.html doc
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page.
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The following coefficients must be defined for each dihedral type via the
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"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
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the data file or restart files read by the "read_data"_read_data.html
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or "read_restart"_read_restart.html commands:
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K (energy)
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n (integer >= 0)
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d (integer value of degrees)
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weighting factor (1.0, 0.5, or 0.0) :ul
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The weighting factor is required to correct for double counting
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pairwise non-bonded Lennard-Jones interactions in cyclic systems or
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when using the CHARMM dihedral style with non-CHARMM force fields.
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With the CHARMM dihedral style, interactions between the 1st and 4th
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atoms in a dihedral are skipped during the normal non-bonded force
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computation and instead evaluated as part of the dihedral using
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special epsilon and sigma values specified with the
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"pair_coeff"_pair_charmm.html command of pair styles that contain
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"lj/charmm" (e.g. "pair_style lj/charmm/coul/long"_pair_charmm.html)
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In 6-membered rings, the same 1-4 interaction would be computed twice
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(once for the clockwise 1-4 pair in dihedral 1-2-3-4 and once in the
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counterclockwise dihedral 1-6-5-4) and thus the weighting factor has
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to be 0.5 in this case. In 4-membered or 5-membered rings, the 1-4
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dihedral also is counted as a 1-2 or 1-3 interaction when going around
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the ring in the opposite direction and thus the weighting factor is
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0.0, as the 1-2 and 1-3 exclusions take precedence.
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Note that this dihedral weighting factor is unrelated to the scaling
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factor specified by the "special bonds"_special_bonds.html command
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which applies to all 1-4 interactions in the system. For CHARMM force
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fields, the special_bonds 1-4 interaction scaling factor should be set
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to 0.0. Since the corresponding 1-4 non-bonded interactions are
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computed with the dihedral. This means that if any of the weighting
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factors defined as dihedral coefficients (4th coeff above) are
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non-zero, then you must use a pair style with "lj/charmm" and set the
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special_bonds 1-4 scaling factor to 0.0 (which is the
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default). Otherwise 1-4 non-bonded interactions in dihedrals will be
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computed twice.
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For simulations using the CHARMM force field with a Coulombic cutoff,
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the difference between the {charmm} and {charmmfsw} styles is in the
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computation of the 1-4 non-bond interactions, though only if the
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distance between the two atoms is within the switching region of the
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pairwise potential defined by the corresponding CHARMM pair style,
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i.e. within the outer cutoff specified for the pair style. The
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{charmmfsw} style should only be used when using the corresponding
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"pair_style lj/charmmfsw/coul/charmmfsw"_pair_charmm.html or
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"pair_style lj/charmmfsw/coul/long"_pair_charmm.html commands. Use
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the {charmm} style with the older "pair_style"_pair_charmm.html
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commands that have just "charmm" in their style name. See the
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discussion on the "CHARMM pair_style"_pair_charmm.html doc page for
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details.
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Note that for AMBER force fields, which use pair styles with "lj/cut",
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the special_bonds 1-4 scaling factor should be set to the AMBER
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defaults (1/2 and 5/6) and all the dihedral weighting factors (4th
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coeff above) must be set to 0.0. In this case, you can use any pair
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style you wish, since the dihedral does not need any Lennard-Jones
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parameter information and will not compute any 1-4 non-bonded
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interactions. Likewise the {charmm} or {charmmfsw} styles are
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identical in this case since no 1-4 non-bonded interactions are
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computed.
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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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[Restrictions:]
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When using run_style "respa"_run_style.html, these dihedral styles
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must be assigned to the same r-RESPA level as {pair} or {outer}.
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When used in combination with CHARMM pair styles, the 1-4
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"special_bonds"_special_bonds.html scaling factors must be set to 0.0.
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Otherwise non-bonded contributions for these 1-4 pairs will be
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computed multiple times.
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These dihedral styles can only be used if LAMMPS was built with the
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MOLECULE package. See the "Build package"_Build_package.html doc page
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for more info.
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[Related commands:]
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"dihedral_coeff"_dihedral_coeff.html
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[Default:] none
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:line
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:link(dihedral-Cornell)
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[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
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Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
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:link(dihedral-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 B, 102, 3586 (1998).
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