Re: [AMBER] Scaling of Non-Bonding Potential for Specific Atom Pairs

From: David A Case <>
Date: Tue, 18 Oct 2016 09:02:06 -0400

On Tue, Oct 18, 2016, Samuel Walpole (PHA) wrote:
> I am looking for a way to scale the non-bonding interactions between
> particular atom types while leaving the potential unchanged for other
> atom types. As an example, I would want to scale the non-bonding
> potential between the solvent and the solute carbon atoms, but keep
> all solvent-solvent, solute-solute and solvent-solute(non-carbon)
> interactions unchanged (or a scaling factor of 1).
> I have found a way to do this for only the Lennard-Jones potential by
> using the changeLJPair function in ParmEd and computing the appropriate
> r and epsilon values for the pair, but haven't found any equivalent
> for the electrostatic potential or the non-bonding potential as a
> whole. Does anyone know how I would implement this in Amber?

You can't do this with the current code; even with code modifications it would
be a big job. The PME procedure puts that charge density onto a grid, and
there is no way to distinguish between "solvent" and "solute" contributions to
that density.

One possibility is to use IPS: this preserves the pairwise character to
electrostatic interactions. So you could go deep into the inner loop, and
apply a scaling depending the nature of the atoms involved.


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Received on Tue Oct 18 2016 - 06:30:05 PDT
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