6.2 Keywords for Generating Non-Bonded Interactions

The key words, their functions, and defaults are:

ATOM

(default) Non-bonded interactions are calculated atom by atom with switching functions being used.

RESI

Non-bonded interactions are determined residue by residue using a rectangular box search. Switching functions are calculated for every atom-atom pair.

SHFT

Non-bonded interactions are calculated atom by atom and the potential is shifted to smooth it at the cutoff.

EXEL

Extended electrostatics using dipoles for all residues outside the CUTNB cutoff.

EXFL

Extended electrostatics using dipoles and quadrupoles for all residues outside the CUTNB limits.

EXNQ

Extended electrostatics to first order without residue quadrupoles.

CONS

Similar to ATOM except a constant dielectric is used.

DUMMy

Generates an empty non-bonded interaction list.

CUTNB

Distance cutoff in generating the list of pairs. The default is 8.0 Angstroms for ATOM, RESI, and SHFT; the default is 5.0 Angstroms for EXFL, EXEL, CONS.

CTOFNB

Distance cut at which the switching function eliminates all contributions from a pair in calculating energies. Once specified, This value is not reset unless respecified. The default is CUTNB-0.5, or CUTNB-0.2 for EXFL and EXEL.

CTONNB

Distance cut at which the smoothing function begins to reduce a pair's contribution. This value is not used with SHFT. Once specified, This value is not reset unless respecified. The defaults is CTOFNB-1.0, or CTOFNB-0.3 for EXFL and EXEL.

CUTMP

Distance cut at which the extended electrostatics routines change from atom by atom evaluation of distant residues to a multipole and polynomial expansion. The default is 0.0.

EPS

Dielectric constant for the extended electrostatics routines (ATOM and RESI options set the dielectric equal to r times the EPS value). The default is 2.5 for constant dielectric, and 1.0 for r dependent dielectric.

VDWO

If VDWO is specified then EPS is set to 0.

WMIN

Warning cutoff for minimum atom to atom distance. Pairs are checked during close contact list compilation using the ATOM, EXEL, EXFL and CONS options. The default is 1.5 Angstroms.

WRNMXD

Warning cutoff for maximum atom displacement from the last close contact list update (used only in EXEL and EXFL). The default is 0.5 Angstroms.