[gmx-users] soft-core and coulomb transformation

David Mobley dmobley at gmail.com
Tue Nov 13 01:17:36 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.

Sorry, what I mean by "charging" versus "discharging" is that
"charging" is where the A state has zero charges and the B state has
normal charges, and discharging is the reverse. So "charging" is the
scenario you describe, and "discharging" is the reverse.


> Berk.
> >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.
> >
> >Thanks,
> >David
> >
> >
> >
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