Dear Mark Here it is some information that may be useful. I checked all my -pd, with distance restraints MD runs. It seemed that crash usually happened when protons and the carbon they attached were in different processors.
best, dawei On Thu, Dec 13, 2012 at 4:12 PM, Da-Wei Li <[email protected]> wrote: > Dear Mark > > Thanks for the quick response. This has bothered me for some time. I feel > something is wrong because > > 1. If I turn off lincs (dt will be 0.001 instead of 0.002 ), I can run > the same simulation for very long (>500 ns) without any problem. By saying > "same simulation", I mean everything is identical except dt (=0.001) and > constraints (= none). Once I turned on lincs (even with dt is still 0.001) > by set constraints to hbonds, the md run will crash from time to time. > > 2. With the help of cpt file (it is a numerical exact re-start because I > don't change anything and I use the same number of processors), I usually > can pass the last time crash point without error. > > best, > > dawei > > > > On Thu, Dec 13, 2012 at 12:17 PM, Mark Abraham > <[email protected]>wrote: > >> 1) AFAIK there are indeed conditions under which domain decomposition does >> not work with distance restraints >> 2) Your symptoms could just be that (some of) your initial conditions, or >> them in combination with the restraints are problematic. Without more >> description about why and how you're using the restraints, and that your >> systems are stable in the absence of restraints, it's hard to say much. >> 3) Generally, turning off the restraints is not a proper solution (and >> particularly not without adjusting the time step accordingly) - see >> http://www.gromacs.org/Documentation/Terminology/Blowing_Up >> 4) We're a long way from supposing there's a code bug :-) >> >> Mark >> >> On Thu, Dec 13, 2012 at 4:40 PM, Da-Wei Li <[email protected]> wrote: >> >> > Dear Gromacs users >> > >> > I recently tried distance restraints simulation and I have been forced >> to >> > use -PD (particle decomposition) because domain decomposition doesn't >> work >> > with distance restraints. However, my MD run will crash randomly for >> some >> > of my proteins but works well for others. Once it is crashes, I try to >> > rescue it by restart it using CPT file. Some times, the simulation can >> pass >> > the crash point and continue for a long time and some times it just keep >> > crashing. The only work-around I found is to turn off lincs. Does this >> mean >> > a bug in the code? I observed this for 4.5 and 4.6. >> > >> > best, >> > >> > dawei >> > -- >> > gmx-users mailing list [email protected] >> > 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 [email protected]. >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
