forked from lijiext/lammps
118 lines
4.6 KiB
Plaintext
118 lines
4.6 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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pair_style lj/charmm/coul/charmm command :h3
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pair_style lj/charmm/coul/charmm/implicit command :h3
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pair_style lj/charmm/coul/long command :h3
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[Syntax:]
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pair_style style args :pre
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style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long}
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args = list of arguments for a particular style :ul
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{lj/charmm/coul/charmm} args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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{lj/charmm/coul/charmm/implicit} args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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{lj/charmm/coul/long} args = inner outer (cutoff)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) :pre
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[Examples:]
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pair_style lj/charmm/coul/charmm 8.0 10.0
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pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
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pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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pair_style lj/charmm/coul/long 8.0 10.0
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pair_style lj/charmm/coul/long 8.0 10.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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[Description:]
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The {lj/charmm} styles compute LJ and Coulombic interactions with an
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additional switching function S(r) that ramps the energy and force
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smoothly to zero between an inner and outer cuoff. It is a widely
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used option in the CHARMM MD code.
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:c,image(Eqs/pair_charmm.jpg)
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Both the LJ and Coulombic terms require an inner and outer cutoff.
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They can be the same for both formulas or different depending on
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whether 2 or 4 arguments are used in the pair_style command. In each
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case, the inner cutoff distance must be less than the outer cutoff.
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It it typical to make the difference between the 2 cutoffs about 1.0
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Angstrom.
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Style {lj/charmm/coul/charmm/implicit} computes the same formulas as
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style {lj/charmm/coul/charmm} except that an additional 1/r term is
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included in the Coulombic formula. The Coulombic energy thus varies
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as 1/r^2. This is effectively a distance-dependent dielectric term
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which is a simple model for an implicit solvent with additional
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screening. It is designed for use in a simulation of an unsolvated
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biomolecule (no explicit water molecules).
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Style {lj/charmm/coul/long} computes the same formulas as style
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{lj/charmm/coul/charmm} except that an additional damping factor is
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applied to the Coulombic term, as in the discussion for pair style
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{lj/cut/coul/long}. Only one Coulombic cutoff is specified for
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{lj/charmm/coul/long}; if only 2 arguments are used in the pair_style
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command, then the outer LJ cutoff is used as the single Coulombic
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cutoff.
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The following coefficients must be defined for each pair of atoms
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types via the "pair_coeff"_pair_coeff.html command as in the examples
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above, or in the data file or restart files read by the
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands:
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epsilon (energy units)
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sigma (distance units)
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epsilon_14 (energy units)
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sigma_14 (distance units) :ul
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Note that sigma is defined in the LJ formula as the zero-crossing
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distance for the potential, not as the energy minimum at 2^(1/6)
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sigma.
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The latter 2 coefficients are optional. If they are specified, they
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are used in the LJ formula between 2 atoms of these types which are
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also first and fourth atoms in any dihedral. No cutoffs are specified
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because this CHARMM force field does not allow varying cutoffs for
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individual atom pairs; all pairs use the global cutoff(s) specified in
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the pair_style command.
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[Restrictions:]
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The {lj/charmm/coul/charmm} and {lj/charmm/coul/charmm/implicit}
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styles are part of the "molecule" package. The {lj/charmm/coul/long}
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style is part of the "kspace" package. They are only enabled if
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LAMMPS was built with those package(s). See the "Making
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LAMMPS"_Section_start.html#2_2 section for more info.
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On some 64-bit machines, compiling with -O3 appears to break the
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Coulombic tabling option used by the {lj/charmm/coul/long} style. See
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the "Additional build tips" section of the Making LAMMPS documentation
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pages for workarounds on this issue.
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[Related commands:]
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"pair_coeff"_pair_coeff.html
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[Default:] none
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