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 <mrshi...@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. > > > > > > On Thu, Sep 26, 2013 at 6:32 PM, Christopher Neale > <chris.ne...@mail.utoronto.ca> wrote: >> My mistake .... I still get a segfault even when using double precision. (EM >> doesn't help, nor does switching to Berendsen pressure coupling). >> >> Note that I can stop the segfault when running at init-lambda-state = 0 if I >> set: >> >> couple-lambda0 = none >> couple-lambda1 = none >> >> instead of >> >> couple-lambda0 = vdw-q >> couple-lambda1 = none >> >> This looks like http://bugzilla.gromacs.org/issues/1306 >> >> Thank you, >> Chris. >> >> -- original message -- >> >> Thank you Mark. >> >> I actually found that it crashed wihout the -multi part (no hamiltonian >> exchange). >> The command that I used was: mdrun -nt 1 -deffnm ethanol.1 -dhdl >> ethanol.1.dhdl.xvg >> >> If I use the double precision version, there is no segfault. That's a >> working solution, but it is worrysome. >> >> Thank you, >> Chris. >> >> -- >> 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