[gmx-users] Re: WCA and free energy calculations
gmx3 at hotmail.com
Mon Jun 25 14:18:37 CEST 2007
>From: "David Mobley" <dmobley at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Re: WCA and free energy calculations
>Date: Mon, 25 Jun 2007 05:00:23 -0700
>>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
>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
Nearly anything can be done now in Gromacs :) (although sometimes not
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
if you want different sigma's), then the free-energy part is trivial.
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