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lammps/doc/special_bonds.txt
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"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
special_bonds command :h3
[Syntax:]
special_bonds keyword values ... :pre
one or more keyword/value pairs may be appended :ulb,l
keyword = {amber} or {charmm} or {fene} or {lj/coul} or {lj} or {coul} or {dihedral} or {extra} :l
{amber} values = none
{charmm} values = none
{fene} values = none
{lj/coul} values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
{lj} values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
{coul} values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
{dihedral} value = {yes} or {no}
{extra} value = N
N = number of extra 1-2,1-3,1-4 interactions to save space for :pre
:ule
Examples:
special_bonds amber
special_bonds charmm
special_bonds fene dihedral no
special_bonds lj/coul 0.0 0.0 0.5 dihedral yes
special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
special_bonds lj/coul 0 1 1 extra 2 :pre
[Description:]
Set weighting coefficients for pairwise energy and force contributions
from atom pairs that are also bonded to each other directly or
indirectly. For Lennard-Jones (LJ) and Coulombic pairwise
interactions, these coefficients come in sets of three. The 1st
coefficient is the weighting factor on 1-2 atom pairs, which are those
directly bonded to each other. The 2nd coefficient is the weighting
factor on 1-3 atom pairs which are those separated by 2 bonds
(e.g. the two H atoms in a water molecule). The 3rd coefficient is
the weighting factor on 1-4 atom pairs which are those separated by 3
bonds (e.g. the 1st and 4th atoms in a dihedral interaction). Thus if
the 1-2 coefficient is set to 0.0, then the pairwise interaction is
effectively turned off for all pairs of atoms bonded to each other.
IMPORTANT NOTE: For purposes of computing weighted pairwise
interactions, 1-3 and 1-4 interactions are not defined from the list
of angles or dihedrals used by the simulation. Rather, they are
inferred topologically from the set of bonds defined when the
simulation is defined from a data or restart file (see
"read_data"_read_data.html or "read_restart"_read_restart.html
commands). Thus the set of 1-2,1-3,1-4 interactions that the weights
apply to is the same whether angle and dihedral potentials are
computed or not, and remains the same even if bonds are constrained,
or turned off, or removed during a simulation.
The two exceptions to this rule are (a) if the {dihedral} keyword is
set to {yes} (see below), or (b) if the
"delete_bonds"_delete_bonds.html command is used with the {special}
option that recomputes the 1-2,1-3,1-4 topologies after bonds are
deleted; see the "delete_bonds"_delete_bonds.html command for more
details.
The {amber} keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
is the default for a commonly used version of the AMBER force field,
where the last value is really 5/6.
The {charmm} keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
LJ and Coulombic interactions, which is the default for a commonly
used version of the CHARMM force field. Note that in pair styles
{lj/charmm/coul/charmm} and {lj/charmm/coul/long} the 1-4 coefficients
are defined explicitly, and these pairwise contributions are computed
as part of the charmm dihedral style - see the
"pair_coeff"_pair_coeff.html and "dihedral_style"_dihedral_style.html
commands for more information.
The {fene} keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
LJ and Coulombic interactions, which is consistent with a
coarse-grained polymer model with "FENE bonds"_bond_fene.html.
The {lj/coul}, {lj}, and {coul} keywords allow the 3 coefficients to
be set explicitly. The {lj/coul} keyword sets both the LJ and
Coulombic coefficients to the same 3 values. The {lj} and {coul}
keywords only set either the LJ or Coulombic coefficients. Use both
of them if you wish to set the LJ coefficients to different values
than the Coulombic coefficients.
The {dihedral} keyword allows the 1-4 weighting factor to be ignored
for individual atom pairs if they are not listed as the first and last
atoms in any dihedral defined in the simulation. For example, imagine
the 1-4 weighting factor is set to 0.5 and you have a linear molecule
with 5 atoms and bonds as follows: 1-2-3-4-5. If your data file
defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
dihedral, then the pairwise interaction between atoms 1 and 4 will
always be weighted by 0.5, but different force fields use different
rules for weighting the pairwise interaction between atoms 2 and 5.
If the {dihedral} keyword is specified as {yes}, then the pairwise
interaction between atoms 2 and 5 will be unaffected (full weighting
of 1.0). If the {dihedral} keyword is specified as {no} which is the
default, then the 2,5 interaction will also be weighted by 0.5.
The {extra} keyword is used when additional bonds will be created
during a simulation run, e.g. by the "fix
bond/create"_fix_bond_create.html command. A list of 1-2,1-3,1-4
neighbors for each atom is calculated and stored by LAMMPS. If new
bonds are created, the list needs to grow. Using the {extra} keyword
leaves empty space in the list for N additional bonds to be added. If
you do not do this, you may get an error when bonds are added.
[Restrictions:] none
[Related commands:]
"delete_bonds"_delete_bonds.html, "fix bond/create"_fix_bond_create.html
[Default:]
All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
dihedral = no, and extra = 0.
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