nbonds <parameter-nbonds-statement> end
<parameter-nbonds-statement> :==
cutnb=<real>
Nonbonded interaction cutoff for list generation.
cutnb >= ctofnb + 2*tolerance. Default=8.5A
group|atom
Exclusive flags: group by group or atom by atom cutoff. Default=atom
tolerance=<real>
Distance that any atom is allowed to move before pairlist is
updated. Default=0.5A
wmin=<real>
Close contact warning distance. Default=1.5A
inhibit=<real>
Distance at which nonbonded interactions are truncated. Default=0.25A
special_position=<real>
Distance at which special positions are flagged. If less than 0
no special positions will be flagged. Default=0.1A
switching/shifting applies to both electrostatic and van der waals terms
ctofnb=<real>
Distance at which the switching function or shifting function
makes the energy zero. Default=7.5A
ctonnb=<real>
Distance at which the switching function becomes effective. Default=6.5A
truncation
No switching or shifting. Energies are computed for atoms less then
cutnb apart.
switch
Electrostatic switching function.
shift
Electrostatic potential shifting function.
shforce
Electrostatic force shifting function.
cdie
Constant dielectric.
rdie
R-dependent dielectric.
e14fac=<real>
Scale factor for 1-4 electrostatic interactions.
vswitch
Enables vdw switching. Activating truncation will turn off switching.
repel=<real>
If greater than 0, turns on repulsive potential & turns off
electrostatics. The value specifies the factor to multiply the
usual vdw radius by. Default=0
Repulsive term:
irex irex rexp
E (R) = Rcon*[(repel*Rmin) - R ]
vdw
where Rmin is the value at which the Lennard-Jones potential
is minimal. Only irex=1,2 and rexp=2,4 are allowed.
rconst=<real>
Force constant for repulsive potential. Default=100.0
attractive-repulsive term options
rattract=<real>
Distance at which attractive-replusive term energy well begins.
nbxmod=[+|-]1|[+|-]2|[+|-]3|[+|-]4|[+|-]5
Mode for nonbonded exclusions:
+-1=exclude nothing
+-2=exclude only 1-2 (bond)
+-3=exclude 1-2 (bond) and 1-3 (angle)
+-4=exclude 1-2 1-3 and 1-4
+-5=same as (4) but use special 1-4 parameters.
A positive mode value causes the explicit nonbonded exclusions (eg. in
aromatic rings) to be added. A negative value causes them to be
discarded.
turning on/off energy terms
Use the flags command to enable/disable the energy terms:
vdw - for van der waals (intra-molecular)
elec - for electrostatic (intra-molecular)
pvdw - for symmetry van der waals
pele - for symmetry electrostatic.