6.2 Keywords for Generating Non-Bonded Interactions
The key words, their functions, and defaults are:
- (default) Non-bonded interactions are calculated atom by atom
with switching functions being used.
- Non-bonded interactions are determined residue by residue using a
rectangular box search. Switching functions are calculated for every atom-atom
- Non-bonded interactions are calculated atom by atom and the potential
is shifted to smooth it at the cutoff.
- Extended electrostatics using dipoles for all residues outside the CUTNB
- Extended electrostatics using dipoles and quadrupoles for all residues outside
the CUTNB limits.
- Extended electrostatics to first order without residue quadrupoles.
- Similar to ATOM except a constant dielectric is used.
- Generates an empty non-bonded interaction list.
- 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.
- 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.
- 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
- 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.
- 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.
- If VDWO is specified then EPS is set to 0.
- 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.
- Warning cutoff for maximum atom displacement from the last close contact
list update (used only in EXEL and EXFL). The default is 0.5