[gmx-users] Free energy calculation problems (bug?)

[Олег Титов]

What should I do to be able to file a redmine? I've registered at
redmine.gromacs.org, but the account is waiting for confirmation for 2
days. Should I do anything else, or it's ok?


2014-02-08 18:49 GMT+04:00 Michael Shirts <mrshirts at gmail.com>:

> Two thoughts that probably don't explain the problem, since they
> should have similar behavior between versions:
>
> * vdw-type                 = Cut-off
>
> is almost never a good idea.  If you are doing this to be
> reproducible, it's fine, but I'd avoid it in the future.
>
> * You almost certainly want DispCorr = EnerPres, or else the density
> will change with cutoff, and dispersion interactions beyond the cutoff
> will be neglected (also changing the energy with cutoff).
>
> Can you file a redmine (http://redmine.gromacs.org) with .top  and
> .gro files as well?  One never knows where a problem might be coming
> from (maybe only with certain top files?), so having those helps as
> well.  It would be better to have the softcore version, since that is
> likely to be better behaved anyway, and it has the same difference.
>
>
> On Sat, Feb 8, 2014 at 12:00 AM, Олег Титов <titovoi at qsar.chem.msu.ru>
> wrote:
> > Dear GROMACS users!
> >
> > I've encountered a problem in thermodynamic integration with GROMACS. I'm
> > interested in calculating of solvation free energy differences between
> > holbenzenes and benzene. To calculate this values I use thermodynamic
> > integration approach (5 point formula).
> >
> > Half a year ago I did my calculation with GROMACS 4.6.1. The results
> looked
> > good and were consistent with literature data. Recently, I've discovered
> > that versions 4.6.0 and 4.6.1 had a bug in free energy code, so I decided
> > to recalculate everything with 4.6.5 version of GROMACS. New results look
> > not so good and, moreover, are not consistent with literature.
> >
> > I use GAFF forcefield with TIP3P water models. To obtain GROMACS topology
> > and coordinate files I convert AMBER topologies (generated with tleap)
> with
> > amb2gmx.pl script and this topologies look fine.
> >
> >  For phenylbromide molecule calculated solvation free difference should
> be
> > near -0.1 - -0.2 kcal/mol (Experimental data is 0.59 kcal/mol).
> > 4.6.1 version gave me -0.1+-0.13 kcal/mol - Fine!
> > I've performed the same calculation with AMBER11  - -0.27 +-0.16
> kcal/mol -
> > also fine.
> > 4.6.5 version for the same system gives me 1.1 - 1.2 kcal/mol
> >
> > I've played with some options (tried adding soft-core potentials and
> turned
> > on/off couple-intramol option). The results are:
> > no_sc no_intramol 1.27 +- 0.18
> > no_sc intramol 1.20 +- 0.20
> > sc no_intramol 1.35 +- 0.21
> > sc intramol 1.22 +- 0.19
> >
> > So now I don't know what to do. Old buggy version produced good results
> > consistent with literature and other MD packages and new fixed version
> > produces different results. The dH/dl curve for two versions of GROMACS
> > looks similar for lambdas 0-0.7 (mutation is PhBr -> PhH ) but becomes
> > different at lambda = 0.9 So something changed there... Moreover
> different
> > elecrostatic approaches for PhBr molecule are consistent with each other
> > (dddG are fine), but new version of GROMACS gives me overestimated ddG as
> > shown above.
> >
> > Can anyone give me some advice what to do with it? May be there is some
> bug
> > in new version? May be I'm doing something wrong?
> >
> > Attaching sample .mdp (for solvated and vacuum system) and .top files.
> >
> > Thanks for the help,
> > Oleg
> >
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