NONBONDED

NAME
NONBONDED - Read Lennard-Jones parameters

SYNOPSIS

NONBONDED [MIXRULE, NOMIXRULE]
   ...
END

DESCRIPTION
The command reads the Lennard-Jones parameters for the solute non-bonded interactions:

$${ A \over r^{12}} - {B \over r^6} = 4 \epsilon \left [ \left ( { \sigma \over r} \right )^{12} - \left ( { \sigma \over r} \right )^{6} \right ]$$ (10.1)

Arguments MIXRULE and NOMIXRULE to the command indicate if Lennard-Jones mixing rules are to be used by ORAC or, conversely, explicit mixed Lennard-Jones potentials are to be expected in input. The format of the nonbonded potential is different in the two alternative cases. If mixing rules are to be found the input to NONBONDED looks like:
NONBONDED MIXRULE
...
typ1 $r_{min}$ $\epsilon$ $\gamma$ $mass$
...
END
Here, typ1 is a character string, not to exceed 7 characters, labeling the atom type for the atom; $r_{min}$ is the radius corresponding to the minimum of the Lennard-Jones potential; $\epsilon$ the Lennard-Jones well depth; $\gamma$ is reserved for later usage and should be set to zero; $mass$ is the atom mass. The non-bonded potential format changes if different Lennard-Jones potentials must be used for the 1-4 interactions in which atom type typ1 is involved:
NONBONDED MIXRULE
...
typ1 $r_{min}$ $\epsilon$ $r_{min}^{14}$ $\epsilon^{14}$ $mass$
...
END
Here, parameters $r_{min}^{14}$ $\epsilon^{14}$ are used only for 1-4 interactions. In case the argument NOMIXRULE is used, the input to NONBONDED looks like:
NONBONDED NOMIXRULE
...
typ1 $r_{min}$ $\epsilon$ $\gamma$ $mass$
...
END
...
$B_{ij}$ $A_{ij}$
...
First the sequence of the $N_{type}$ force field atom types and Lennard-Jones parameters is read interrupted by the keyword END at the beginning of a new line. Second, a list of the $N_{type} \left ( N_{type} +1 \right ) / 2$ interaction potential parameters $B$ and $A$ must be provided in input. For most of the biomolecular force fields non-bonded mixing rules are commonly used.

EXAMPLES 1

NONBONDED MIXRULE
h4      1.409   0.015   0.000   1.008 
o       1.661   0.210   0.000  16.000 
ca      1.908   0.086   0.000  12.010 
END

EXAMPLES 2

NONBONDED NOMIXRULE
h       0.000   0.000   0.000   1.008 
o       1.700   0.120   0.000  15.999
c       2.000   0.110   0.000  12.011 
END
0.0      0.0        Interaction type [h -- h]
0.0      0.0        Interaction type [h -- o]
0.0      0.0        Interaction type [h -- c]
1200.0   600700.0   Interaction type [o -- o]
1000.0   800000.0   Interaction type [o -- c]
2000.0   500100.0   Interaction type [c -- c]

WARNINGS
If the 1-4 interaction parameters are not provided in input to NONBONDED MIXRULE, the regular non-bonded parameters multiplied by the 1-4 factor LJ-FUDGE (see environment &POTENTIAL) are used instead. For interactions involving one atom for which the 1-4 parameters are given and another for which they are not, regular non-bonded parameters for the interaction are used multiplied by the eventual LJ-FUDGE factor.