[gmx-users] free energy with TIP4P bug fixed
dmobley at gmail.com
Thu Jan 29 17:32:26 CET 2009
Yes, I could use clarification here as well.
I had previously suspected a specific bug relating to the free energy
code and water models (TIP4P-Ew) and contacted the list about this a
few weeks ago. At that time Berk told me that there was no
water-specific free energy code, which I take to mean that either (a)
any bug relating to free energies and water models would affect all
water models, and/or (b) any bug relating to a specific water model
would occur both with and without free energy turned on.
Berk, can you please clarify?
> 3. Combining TIP4P and the free-energy code with at least 3 energy groups
> (TIP4P, perturbed atoms, rest of system) will not lead to the errors noted.
> This would only require 2 energy groups if the system was composed of only
> TIP4P and the perturbed atoms.
I also need clarification here. Do the perturbed atoms have to
comprise a separate group?
> It would be very useful for me if somebody could validate the statements
> above or state any incorrections in those statements.
> Thank you,
> -- original message --
> 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
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