LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands

### special_bonds command

Syntax:

    special_bonds keyword values ...

- one or more keyword/value pairs may be appended
- keyword = amber or charmm or fene or lj/coul or lj or coul or dihedral or extra

        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

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

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 or read_restart 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 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 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 and dihedral_style 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.

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 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, fix bond/create

Default:

All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0, dihedral = no, and extra = 0.