The implementation of BAR in gromacs is pretty hard for me to follow because of how everything is stored noncompactly in the histogram. In 4.6, both can be computed from the same dhdl.xvg file, so it might be easier to track down possible bugs.
On Fri, Jun 29, 2012 at 2:24 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Hi, > > we've been trying to do free energy calculations for solvation of two small > molecules in water, n-butylamine (NBA) and diethyl-ether (DEE). For one of > them the result with BAR (using Justin's tutorial) is significantly > different from TI: > BAR TI Exper. (kJ/mol) > NBA -11.1 -10.8 -17.9 > DEE -11.0 -1.8 -7.4 > > Since for NBA the results are pretty close it seems that the protocol should > be right, and the numbers seem to have converged pretty good as well. > > Any clues why these results could be so different? > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
