Hi, David- Perhaps we can work with you to compare the internal g_bar implementation with our external BAR and MBAR implementation run from the .dhdl.xvg data output in 4.6. It would probably be easier to run these calculations after the optimization updates are added in the next few days(?), but we can plan now. Note that withe errors this big, 100-200 ps should be enough to see what's going on, so it can be done rapidly. Drop me a line off the list to figure out details?
Best, Michael On Fri, Aug 24, 2012 at 9:22 AM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Hi, > > we have terrible problems to get reasonable results from BAR free energy > calculations. We basically follow Justin's tutorial for solvation of > methanol, ethanol, diethyl-ether and neopentane in water using OPLS but get > very strange results. The free energy curves are here: > > http://folding.bmc.uu.se/images/koko.jpg > > Molecule Energy Exper > Methanol -8 -21 > Ethanol -9 -21 > Diethylether -11 -7 > Neopentane -10 +11 > > any clue? > -- > 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
