[gmx-users] TIP4P/TIP4P-Ew bug potentially affecting all calculations done with TIP4P with some (few?) exceptions
dmobley at gmail.com
Thu Jan 29 16:28:11 CET 2009
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.
Department of Chemistry
University of New Orleans
Begin forwarded message:
> From: Berk Hess <gmx3 at hotmail.com>
> Date: January 29, 2009 4:21:41 AM CST
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>, <chris.neale at utoronto.ca
> >, <dmobley at gmail.com>
> Subject: free energy with TIP4P bug fixed
> The Coulomb energy difference that Chris Neale observed recently
> was caused by a bug in the neighborlist assignment with the
> of free energy and tip4p water optimization.
> This bug would cause a few tip4p-tip4p charge interactions to be
> 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
> 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
> versions, you can simply put the perturbed atoms and tip4p in
> separate energy groups.
> What can you do with the new Windows Live? Find out
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