From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: "Discussion list for GROMACS users" <[email protected]>
Subject: Re: [gmx-users] Re: WCA and free energy calculations
Date: Mon, 25 Jun 2007 05:00:23 -0700
Berk,
Tabulated bonded potentials work fine with free-energy!
Or have you tried and they did not work?
Just to clarify -- it's not just an issue of free energy. We want to
do free energy calculations using the WCA separation and soft core
potentials.
Since tabulated nonbonded interactions work based on tabulating
interactions as a function of the distance between particles, but soft
core potentials modulate the effective distance between soft core
particles and other particles, it seemed to me there was no way to
implement soft core potentials using tabulated nonbonded interactions
(since not all particles will be soft core particles, so one would
need different interaction tables for different atoms). Am I mistaken?
If so, how would you go about doing this?
If this can be done, then we can do the WCA separation with soft core,
and there's no problem. But if it can't be done, then we're out of
luck.
David
Nearly anything can be done now in Gromacs :) (although sometimes not
easily).
Maybe I missed something, but according to me it should work.
Tabulated potentials work just like any other potential.
So they are soft-cored when the LJ-parameters or charge of one of
the two atoms in the pair interaction is different in state A and B.
So if you have the WCA potential set up propely (maybe using
energygrp-tables
if you want different sigma's), then the free-energy part is trivial.
Berk.
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