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
