forked from lijiext/lammps
113 lines
4.1 KiB
Plaintext
113 lines
4.1 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,Section_commands.html#comm)
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:line
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dihedral_style charmm command :h3
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dihedral_style charmm/omp command :h3
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[Syntax:]
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dihedral_style charmm :pre
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[Examples:]
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dihedral_style charmm
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dihedral_coeff 1 120.0 1 60 0.5 :pre
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[Description:]
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The {charmm} dihedral style uses the potential
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:c,image(Eqs/dihedral_charmm.jpg)
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See "(MacKerell)"_#MacKerell for a description of the CHARMM force
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field. This dihedral style can also be used for the AMBER force field
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(see comment on weighting factors below). See "(Cornell)"_#Cornell
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for a description of the AMBER force field.
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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 (0.0 to 1.0) :ul
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The weighting factor is applied to pairwise interaction between the
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1st and 4th atoms in the dihedral, which are computed by a CHARMM
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"pair_style"_pair_charmm.html with epsilon and sigma values specified
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with a "pair_coeff"_pair_charmm.html command. Note that this
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weighting factor is unrelated to the weighting factor specified by the
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"special bonds"_special_bonds.html command which applies to all 1-4
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interactions in the system.
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For CHARMM force fields, the special_bonds 1-4 weighting factor should
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be set to 0.0. This is because the pair styles that contain "charmm"
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(e.g. "pair_style lj/charmm/coul/long"_pair_charmm.html) define extra
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1-4 interaction coefficients that are used by this dihedral style to
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compute those interactions explicitly. This means that if any of the
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weighting factors defined as dihedral coefficients (4th coeff above)
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are non-zero, then you must use a charmm pair style. Note that if you
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do not set the special_bonds 1-4 weighting factor to 0.0 (which is the
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default) then 1-4 interactions in dihedrals will be computed twice,
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once by the pair routine and once by the dihedral routine, which is
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probably not what you want.
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For AMBER force fields, the special_bonds 1-4 weighting factor should
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be set to the AMBER defaults (1/2 and 5/6) and all the dihedral
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weighting factors (4th coeff above) should be set to 0.0. In this
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case, you can use any pair style you wish, since the dihedral does not
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need any 1-4 information.
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:line
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Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
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the same as the corresponding style without the suffix. They have
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been optimized to run faster, depending on your available hardware, as
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discussed in "Section_accelerate"_Section_accelerate.html of the
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manual. 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 USER-CUDA, GPU, USER-OMP and OPT
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packages, respectively. They are only enabled if LAMMPS was built with
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those packages. See the "Making LAMMPS"_Section_start.html#start_3
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section 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"_Section_start.html#start_6 when you invoke LAMMPS, or you can
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use the "suffix"_suffix.html command in your input script.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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:line
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[Restrictions:]
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This dihedral style can only be used if LAMMPS was built with the
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MOLECULAR package (which it is by default). See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info on packages.
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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(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(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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