[gmx-users] soft-core and coulomb transformation

Berk Hess gmx3 at hotmail.com
Mon Nov 12 22:22:32 CET 2007


But what do you mean with charging and discharging?

Going one way or the other in lambda does not matter.
What matters is if there are particles that have zero charge
in the A-state topology, while they have a non-zero charge
in the B-state topology.


>From: "David Mobley" <dmobley at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "bharat v. adkar" <bharat at sscu.iisc.ernet.in>
>CC: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] soft-core and coulomb transformation
>Date: Mon, 12 Nov 2007 10:26:37 -0800
>Following up on this issue, discharging phenol in water appears to
>give the same results as charging phenol in water. In other words, so
>far the only cases for which there seem to be a problem are relative
>calculations (and so far I haven't looked at this for any other than
>Bharat's test cases).
>Bharat, be sure you submit a bugzilla and we'll see how things go from
>there. I may at some point try setting up some of my own relative free
>energy topologies and see if I see the same effects, but I'm not
>likely to have time for that for a couple days.

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