Thanks for the input and useful information, Jeroen. I am trying to parameterize some new molecules for use in my future work, so I would like to take as much care as possible in getting things right!
-Justin Quoting van Bemmelen <[EMAIL PROTECTED]>: > Hi Justin, > > I can understand that you want your "forward" and "reverse" direction > results to be equal for verification reasons. But keep in mind that > there really is no "forward" or "reverse" direction when doing TI on > separately equilibrated (i.e. independent for every lambda) starting > stuctures (which is IMHO the right way do do TI, btw). There is no > physical reason to check whether both directions give equal results; a > simulation for lambda=0.35 in the forward direction is (or should be) > exactly equivalent to a simulation for lambda=0.65 in the reverse > direction, except for the sign of d(lambda). There is only a > computational reason, obviously, since it helps finding code bugs. ;-) > > So if the "forward" direction is working fine (which I believe it is), > than you don't really need this patch. Simply make sure that your > topologies are consistently defined in that direction. > > Having said that, and taking my first sentence into account, you could > try downloading the 3.3 CVS version. From the information Berk has given > in bug 175, I'm guessing the code was changed somewhere in pme.c, > nb_free_energy.c or force.c. So you may want to 'diff' those with the > 3.3.1 files and alter them accordingly. But since I'm not an expert on > the code, I could be wrong about the files. > > Cheers, > Jeroen > > > >Date: Sun, 17 Feb 2008 17:12:57 -0500 > >From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > >Subject: [gmx-users] Patch for PME in Free Energy? > >To: gmx-users@gromacs.org > >Message-ID: <[EMAIL PROTECTED]> > >Content-Type: text/plain; charset=ISO-8859-1 > > > >Hi all, > > > >I guess this is directed towards the developers. Thanks to > >David Mobley, I was > >able to determine that my free energy calculations were victim > >of a PME bug in > >version 3.3.1. In the Bugzilla, Berk commented that the issue had been > >resolved for the upcoming release of versions 3.3.3 and 4.0, > >so I'm guessing > >the issue remains in version 3.3.2? If so, is there a > >modification I can make > >to any source code files (either version 3.3.1 or 3.3.2) so I > >can re-compile, > >or should I just be patient and wait for version 3.3.3? > > > >Thanks, > >Justin > _______________________________________________ > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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