Hi,
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.
Berk.
From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: "bharat v. adkar" <[EMAIL PROTECTED]>
CC: Discussion list for GROMACS users <[email protected]>
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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