Syntax:
special_bonds style special_bonds c1 c2 c3 special_bonds c1 c2 c3 c4 c5 c6
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).
1-3, and 1-4 interactions are not computed using the list of angles and dihedrals defined in the simulation. Rather, they are inferred by the set of defined bonds. This distinction is important to remember if bonds are removed at some point during a simulation. Also note that turning off a bond (as opposed to removing it) does not change the inference of 1-2, 1-3, and 1-4 neighbors. See the delete_bonds 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:
Default:
special_bonds 0.0 0.0 0.0