Berk, > 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. David > Berk. > > > >From: "David Mobley" <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org> > >To: "bharat v. adkar" <[EMAIL PROTECTED]> > >CC: Discussion list for GROMACS users <gmx-users@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 > > > > > > > > > _________________________________________________________________ > Play online games with your friends with Messenger > http://www.join.msn.com/messenger/overview > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
