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? Thanks, David > It would be very useful for me if somebody could validate the statements > above or state any incorrections in those statements. > > Thank you, > Chris. > > > > > > -- original message -- > > 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 > > > _______________________________________________ > gmx-users mailing list [email protected] > 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 thewww interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
