lammps/doc/special_bonds.txt

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special_bonds command :h3

[Syntax:]

special_bonds style args :pre

style = {charmm} or {amber} or {dihedral} or {explicit} ({explicit} can be omitted) :ulb,l
  {charmm} args = none
  {amber} args = none
  {dihedral} args = c1 c2 c3 c4 c5 c6
    c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified)
    c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional)
  {explicit} args = c1 c2 c3 c4 c5 c6
    c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified)
    c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional) :pre
:ule

Examples:

special_bonds charmm
special_bonds amber
special_bonds dihedral 0.0 0.0 0.5
special_bonds explicit 0 1 1
special_bonds 0 1 1
special_bonds 0.0 0.0 1.0 0.0 0.0 0.5 :pre

[Description:]

Set the weighting coefficients for the pairwise force and energy
contributions from atom pairs that are also bonded to each other
directly or indirectly.  For Lennard-Jones and Coulombic pairwise
interactions, 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 2 H atoms in a water molecule).  The
3rd coefficient is the weighting factor on 1-4 atom pairs which are
separated by 3 bonds (e.g. the 1st and 4th atoms in a dihedral
interaction).

Note that 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 by the set of bonds defined when atoms are read in from
a file ("read_data"_read_data.html or
"read_restart"_read_restart.html).  Thus the set of 1-2,1-3,1-4
interactions 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 special_bonds
{dihedral} style is used (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 {charmm} style sets all 3 coefficients to 0.0 for both LJ and
Coulombic interactions, which is the default for the CHARMM force
field.  In pair styles {lj/charmm/coul/charmm} and
{lj/charmm/coul/long} the 1-4 coefficients are defined explicitly, and
these pair-wise contributions are computed in the charmm dihedral
style - see the "pair_coeff"_pair_coeff.html and
"dihedral_style"_dihedral_style.html commands for more information.

The {amber} style 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 particular version of the AMBER force field,
where the last value is really 5/6.

The {dihedral} style requires you to set 3 or 6 coefficients (see the
{explicit} style), but it turns off the 1-4 weighting factor 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
you have set the 1-4 weighting factor 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 be
weighted by 0.5, but the interaction between atoms 2 and 5 will be
unaffected (full weighting of 1.0).  Note that if any of the other
special_bond styles are used, then the 2,5 interaction would also be
weighted by 0.5.  The {dihedral} style is provided because some force
fields follow this rule.

The {explicit} style requires you to set 3 or 6 coefficients directly.
If 3 are specified, they are used for both LJ and Coulombic
interactions.  If 6 are specified then the first 3 are LJ coefficients
and the second 3 are Coulombic coefficients.  Note that the {explicit}
keyword itself is optional; the special_bonds command can just take 3
or 6 numeric arguments by themselves.

IMPORTANT NOTE: For a "lj units"_units.html system with "FENE
bonds"_bond_fene.html a setting of special bonds 0 1 1 should be used.

[Restrictions:] none

[Related commands:]

"delete_bonds"_delete_bonds.html

[Default:]

special_bonds 0.0 0.0 0.0 :pre