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### special_bonds command

Syntax:

    special_bonds style
    special_bonds c1 c2 c3
    special_bonds c1 c2 c3 c4 c5 c6

- style = charmm or amber
- c1,c2,c3,c4,c5,c6 = numeric coefficients from 0.0 to 1.0

Examples:

    special_bonds charmm
    special_bonds amber
    special_bonds 0.0 0.0 1.0
    special_bonds 0.0 0.0 1.0 0.0 0.0 0.5

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. 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 or read_restart). Thus the set of 1-2,1-3,1-4 interactions is the same whether angle potentials are computed or not, and remains the same even if bonds are constrained, or turned off, or removed during a simulation. The only exception is if the delete_bonds command is used with the special option that recomputes the 1-2,1-3,1-4 topologies; see the command for more details.

The charmm style sets all 3 coefficients to 0.0, 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 and dihedral_style 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 0.833 for Coulombic interactions, which is the default for a particular version of the AMBER force field, where the last value is 5/6.

A special_bonds command with 3 coefficients sets the 1-2, 1-3, and 1-4 coefficients for both LJ and Coulombic terms to those values.

A special_bonds command with 6 coefficients sets the 1-2, 1-3, and 1-4 LJ coefficients to the first 3 values and the Coulombic coefficients to the last 3 values.

Restrictions: none

Related commands:

delete_bonds

Default:

    special_bonds 0.0 0.0 0.0