Sounds like we've resolved all the confusion. Thanks for prompt help in making this clearer and better.
On Thu, Sep 26, 2013 at 7:01 PM, Christopher Neale <chris.ne...@mail.utoronto.ca> wrote: > Agreed, the following parameters do not segfault in single or double > precision: > sc-alpha = 0.5 > sc-power = 1 > sc-r-power = 6 > Same goes for http://bugzilla.gromacs.org/issues/1306 > > The following parameters give a segfault in single precision but are ok in > double precision > sc-alpha = 0.001 > sc-power = 1 > sc-r-power = 48 > Same goes for http://bugzilla.gromacs.org/issues/1306 > > Sorry for the confusion earlier. I was using a compilation that I thought was > double precision > but it was actually single. Recompiling in double precision gave me the > stability outlined above. > > Thank you for your assitance Mark and Michael. > > Chris. > > -- original message -- > > Michael Shirts mrshirts at gmail.com > Fri Sep 27 00:41:17 CEST 2013 > Previous message: [gmx-users] segfault when running the alchemistry.org > ethanol solvation free energy tutorial > Next message: [gmx-users] segfault when running the alchemistry.org ethanol > solvation free energy tutorial > Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > And with this change, single is running fine as well. > > This was a known issue, but was only documented in the expanded.mdp > files, which was an oversight. After this, I switched so the default > is less likely to cause problems. Because of some theory improvements > developed in the group in free energy calculation pathways, the > sc-r-power=48 pathway will now be phased out anyway by 5.1. > > On Thu, Sep 26, 2013 at 6:37 PM, Michael Shirts <mrshirts at gmail.com> wrote: >> I thought I had just managed to solve the issue :) >> >> If you look at the soft core parameters, there are two types listed -- >> one with sc-r-power = 48, and one with sc-r-power = 6. The sc-r-power >> are more stable with single precision calculations. >> >> I have changed the files on the website to make the single precision >> ones the default. Expanded.mdp warned about the issues with >> precision, but left the sc-r-power in place; the Ethanol.mdp did not >> warn about the potential issue. Now both include the more efficient >> path commented out. >> >> NOTE that this means the exact numbers of the tutorials are not quite >> right anymore; the process is unchanged, as is the final answer, but >> the intermediate dG's will be slightly different. >> >> However, I need to redo them anyway to make them easier in the next >> 1-2 weeks, so I will update them then. >> >> If it still fails with double, that's a different issue -- because I'm >> running them fine with double. >> >> > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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 * 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