All,
I just wanted to pass along the below e-mail, previously sent to the
mailing list, and highlight the potential implications.
If I understand properly, there was a bug in all Gromacs versions
beginning prior to 3.3 (probably not 3.1.4) and through 4.0.3 that
affected the TIP4P and TIP4P-Ew water models, *unless* you were using
separate energy groups for water and the rest of your system. Berk
notes below that the bug "would cause a few tip4p-tip4p charge
interactions to be missing". I want to emphasize that this is
potentially an extremely serious problem.
In my own testing I found that with this bug, densities for TIP4P-Ew
still came out close to the literature values, but it could result in
substantial errors in other properties. For example, in computing
hydration free energies with acetamide, I found my hydration free
energies changed by more than 2 kcal/mol when I changed rcoulomb by
0.1 nm, even when using PME and long-ish real-space cutoffs, which
should not be the case.
Secondarily, I found that my computed hydration free energies with
either set of cutoffs disagreed with the "correct" values (as obtained
by other simulation packages) by 0.7 to 3 kcal/mol depending on my
choice of real-space cutoff. In contrast, with other water models, I
could reproduce the expected values to within my computed
uncertainties (+/-0.05 to 0.1 kcal/mol).
I am still doing some testing, but I anticipate that I will ultimately
have to submit errata for two different papers I've published in which
I used the TIP4P-Ew water model in combination with GROMACS. I urge
you to check your own studies that have used TIP4P/TIP4P-Ew and see if
they are affected.
David Mobley
Assistant Professor
Department of Chemistry
University of New Orleans
Begin forwarded message:
From: Berk Hess <g...@hotmail.com>
Date: January 29, 2009 4:21:41 AM CST
To: Discussion list for GROMACS users <gmx-users@gromacs.org>, <chris.ne...@utoronto.ca
>, <dmob...@gmail.com>
Subject: free energy with TIP4P bug fixed
Hi,
The Coulomb energy difference that Chris Neale observed recently
was caused by a bug in the neighborlist assignment with the
combination
of free energy and tip4p water optimization.
This bug would cause a few tip4p-tip4p charge interactions to be
missing.
I think it has been present in all Gromacs version which have tip4p
optimized loops,
for sure it was in 3.3.
I have fixed this for the upcoming Gromacs 4.0.4 release.
I assume this bug also caused the cut-off dependence that David
Mobley observed.
I have done a lot of free energy calculation with tip4p and never
noticed
any problems. This was because I always had the perturbed molecule
in a separate energy group, which circumvents the problem.
So for the moment and for checking if you had the problem with older
Gromacs
versions, you can simply put the perturbed atoms and tip4p in
separate energy groups.
Berk
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