AMBER Archive (2006)

Subject: Re: AMBER: About Lennard-Jones Parameters

From: David A. Case (case_at_scripps.edu)
Date: Fri Sep 15 2006 - 19:07:35 CDT

On Fri, Sep 15, 2006, Jianhui wrote:
>
> In parm99.dat file, listed are the van der waals radius sigma and the well
> depth epsilon of different elements, which is used for the same element
> Lennard-Jones interactions such as O-O. How do AMBER calculate the
> Lennard-Jones parameters for different element interaction such as Na-O?
>

This is actually not written down all that often, even in the force field
papers. Here is the relevant code (from
$AMBERHOME/src/leap/src/leap/mathop.c):

/*
 * MathOpConvertNonBondToAC
 *
 * Author: Christian Schafmeister (1991)
 *
 * Convert a pair of nonbond parameters dE1, dR1 and dE2, dR2 to
 * a set of A and C for a non-bond interaction.
 */
void
MathOpConvertNonBondToAC( double dE1, double dR1, double dE2, double dR2,
        double *dPA, double *dPC )
{
double dE, dR, dR6, dER6;

    dR = dR1 + dR2;
    dE = sqrt( dE1 * dE2 );
    dR6 = pow6(dR);
    dER6 = dE*dR6;
    *dPC = 2.0*dER6; /* C = 2*dE*dR^6 */
    *dPA = dER6*dR6; /* A = dE*dR^12 */
}

In words: the two R* values are added together; the epsilon is the geometric
mean of the two epsilon values. Then A anc C are computed from the formulas
above.

...hope this helps....dac

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