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
