[gmx-users] RE: Patch for PME in Free Energy?

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 18 03:33:56 CET 2008

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!


Quoting van Bemmelen <J.J.M.vanBemmelen at student.TUDelft.NL>:

> 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" <jalemkul at vt.edu>
> >Subject: [gmx-users] Patch for PME in Free Energy?
> >To: gmx-users at gromacs.org
> >Message-ID: <1203286377.47b8b1694675b at webmail.vt.edu>
> >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 at 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 gmx-users-request at gromacs.org.
> 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
jalemkul at vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list