forked from lijiext/lammps
204 lines
9.3 KiB
Plaintext
204 lines
9.3 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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special_bonds command :h3
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[Syntax:]
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special_bonds keyword values ... :pre
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one or more keyword/value pairs may be appended :ulb,l
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keyword = {amber} or {charmm} or {dreiding} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} or {extra} :l
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{amber} values = none
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{charmm} values = none
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{dreiding} values = none
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{fene} values = none
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{lj/coul} values = w1,w2,w3
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w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
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{lj} values = w1,w2,w3
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w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
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{coul} values = w1,w2,w3
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w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
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{angle} value = {yes} or {no}
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{dihedral} value = {yes} or {no}
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{extra} value = N
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N = number of extra 1-2,1-3,1-4 interactions to save space for :pre
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:ule
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Examples:
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special_bonds amber
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special_bonds charmm
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special_bonds fene dihedral no
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special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
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special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
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special_bonds lj/coul 0 1 1 extra 2 :pre
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[Description:]
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Set weighting coefficients for pairwise energy and force contributions
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between pairs of atoms that are also permanently bonded to each other,
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either directly or via one or two intermediate bonds. These weighting
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factors are used by nearly all "pair styles"_pair_style.html in LAMMPS
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that compute simple pairwise interactions. Permanent bonds between
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atoms are specified by defining the bond topology in the data file
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read by the "read_data"_read_data.html command. Typically a
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"bond_style"_bond_style.html command is also used to define a bond
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potential. The rationale for using these weighting factors is that
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the interaction between a pair of bonded atoms is all (or mostly)
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specified by the bond, angle, dihedral potentials, and thus the
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non-bonded Lennard-Jones or Coulombic interaction between the pair of
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atoms should be excluded (or reduced by a weighting factor).
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IMPORTANT NOTE: These weighting factors are NOT used by "pair
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styles"_pair_style.html that compute many-body interactions, since the
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"bonds" that result from such interactions are not permanent, but are
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created and broken dynamically as atom conformations change. Examples
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of pair styles in this category are EAM, MEAM, Stillinger-Weber,
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Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no
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sense to define permanent bonds between atoms that interact via these
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potentials, though such bonds may exist elsewhere in your system,
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e.g. when using the "pair_style hybrid"_pair_hybrid.html command.
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Thus LAMMPS ignores special_bonds settings when manybody potentials
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are calculated.
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The Coulomb factors are applied to any Coulomb (charge interaction)
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term that the potential calculates. The LJ factors are applied to the
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remaining terms that the potential calculates, whether they represent
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LJ interactions or not. The weighting factors are a scaling
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pre-factor on the energy and force between the pair of atoms. A value
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of 1.0 means include the full interaction; a value of 0.0 means
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exclude it completely.
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The 1st of the 3 coefficients (LJ or Coulombic) is the weighting
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factor on 1-2 atom pairs, which are pairs of atoms directly bonded to
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each other. The 2nd coefficient is the weighting factor on 1-3 atom
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pairs which are those separated by 2 bonds (e.g. the two H atoms in a
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water molecule). The 3rd coefficient is the weighting factor on 1-4
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atom pairs which are those separated by 3 bonds (e.g. the 1st and 4th
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atoms in a dihedral interaction). Thus if the 1-2 coefficient is set
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to 0.0, then the pairwise interaction is effectively turned off for
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all pairs of atoms bonded to each other. If it is set to 1.0, then
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that interaction will be at full strength.
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IMPORTANT NOTE: For purposes of computing weighted pairwise
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interactions, 1-3 and 1-4 interactions are not defined from the list
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of angles or dihedrals used by the simulation. Rather, they are
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inferred topologically from the set of bonds specified when the
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simulation is defined from a data or restart file (see
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands). Thus the set of 1-2,1-3,1-4 interactions that the weights
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apply to is the same whether angle and dihedral potentials are
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computed or not, and remains the same even if bonds are constrained,
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or turned off, or removed during a simulation.
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The two exceptions to this rule are (a) if the {angle} or {dihedral}
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keywords are set to {yes} (see below), or (b) if the
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"delete_bonds"_delete_bonds.html command is used with the {special}
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option that recomputes the 1-2,1-3,1-4 topologies after bonds are
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deleted; see the "delete_bonds"_delete_bonds.html command for more
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details.
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The {amber} keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
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interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
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is the default for a commonly used version of the AMBER force field,
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where the last value is really 5/6. See "(Cornell)"_#Cornell for a
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description of the AMBER force field.
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The {charmm} keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
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LJ and Coulombic interactions, which is the default for a commonly
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used version of the CHARMM force field. Note that in pair styles
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{lj/charmm/coul/charmm} and {lj/charmm/coul/long} the 1-4 coefficients
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are defined explicitly, and these pairwise contributions are computed
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as part of the charmm dihedral style - see the
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"pair_coeff"_pair_coeff.html and "dihedral_style"_dihedral_style.html
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commands for more information. See "(MacKerell)"_#MacKerell for a
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description of the CHARMM force field.
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The {dreiding} keyword sets the 3 coefficients to 0.0, 0.0, 1.0 for both
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LJ and Coulombic interactions, which is the default for the Dreiding
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force field, as discussed in "(Mayo)"_#Mayo.
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The {fene} keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
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LJ and Coulombic interactions, which is consistent with a
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coarse-grained polymer model with "FENE bonds"_bond_fene.html. See
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"(Kremer)"_#Kremer for a description of FENE bonds.
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The {lj/coul}, {lj}, and {coul} keywords allow the 3 coefficients to
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be set explicitly. The {lj/coul} keyword sets both the LJ and
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Coulombic coefficients to the same 3 values. The {lj} and {coul}
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keywords only set either the LJ or Coulombic coefficients. Use both
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of them if you wish to set the LJ coefficients to different values
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than the Coulombic coefficients.
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The {angle} keyword allows the 1-3 weighting factor to be ignored for
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individual atom pairs if they are not listed as the first and last
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atoms in any angle defined in the simulation or as 1,3 or 2,4 atoms in
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any dihedral defined in the simulation. For example, imagine the 1-3
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weighting factor is set to 0.5 and you have a linear molecule with 4
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atoms and bonds as follows: 1-2-3-4. If your data file defines 1-2-3
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as an angle, but does not define 2-3-4 as an angle or 1-2-3-4 as a
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dihedral, then the pairwise interaction between atoms 1 and 3 will
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always be weighted by 0.5, but different force fields use different
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rules for weighting the pairwise interaction between atoms 2 and 4.
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If the {angle} keyword is specified as {yes}, then the pairwise
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interaction between atoms 2 and 4 will be unaffected (full weighting
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of 1.0). If the {angle} keyword is specified as {no} which is the
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default, then the 2,4 interaction will also be weighted by 0.5.
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The {dihedral} keyword allows the 1-4 weighting factor to be ignored
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for individual atom pairs if they are not listed as the first and last
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atoms in any dihedral defined in the simulation. For example, imagine
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the 1-4 weighting factor is set to 0.5 and you have a linear molecule
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with 5 atoms and bonds as follows: 1-2-3-4-5. If your data file
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defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
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dihedral, then the pairwise interaction between atoms 1 and 4 will
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always be weighted by 0.5, but different force fields use different
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rules for weighting the pairwise interaction between atoms 2 and 5.
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If the {dihedral} keyword is specified as {yes}, then the pairwise
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interaction between atoms 2 and 5 will be unaffected (full weighting
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of 1.0). If the {dihedral} keyword is specified as {no} which is the
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default, then the 2,5 interaction will also be weighted by 0.5.
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The {extra} keyword is used when additional bonds will be created
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during a simulation run, e.g. by the "fix
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bond/create"_fix_bond_create.html command. A list of 1-2,1-3,1-4
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neighbors for each atom is calculated and stored by LAMMPS. If new
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bonds are created, the list needs to grow. Using the {extra} keyword
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leaves empty space in the list for N additional bonds to be added. If
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you do not do this, you may get an error when bonds are added.
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[Restrictions:] none
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[Related commands:]
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"delete_bonds"_delete_bonds.html, "fix bond/create"_fix_bond_create.html
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[Default:]
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All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
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angle = no, dihedral = no, and extra = 0.
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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(Kremer)
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[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).
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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, 102, 3586 (1998).
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:link(Mayo)
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[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
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(1990).
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