On 05/11/2011 05:20 AM, Mark Abraham wrote: > On 05/11/2011 02:32 AM, SebastianWaltz wrote: >> Dear GROMACS User, >> >> I'm running a REMD MD of 32 replicas. It worked for the first few >> replica exchanges. After 30ps again two replicas were exchanged and I >> received the Error: >> x particles communicated to PME node y are more than a cell length out >> of the domain decomposition cell of their charge group > > The only rationale I can see is that a velocity was scaled after > exchange that was now large enough to lead to the normal sort of > exploding system. Was the exploding replica going up in temperature? > How did you equilibrate the systems? I did a NPT equilibration for each replica which leads obviously to different volumes and looks like to cause some problems. If I use the same volume for each replica it works fine. > >> I am using NVT assembles for each replica with a exchanging interval of >> 5ps. For each replica I use 4 processors. Constraint are only the bonds >> to hydrogens (constraints = hbonds). Using PME for electro static. > > Information like GROMACS version, simulation system dimensions and > contents would be useful. What replica temperature distribution exists? I am using version 4.0.7. My system consists of a small peptide soluted in ~1500 rigid CHCl3 molecules. System equilibrated with NPT and NVT production run seems to work only if I increase the number of replicas (32->64) meaning that I also decrease the difference of the volumes. The temperature is exponentially distributed from 200 to 450K. > >> When running each replica for its own everything is working fine, >> nothing is blowing up like one would expect after getting the above >> Error. > > Good trouble-shooting :) You'd have been told to try this otherwise... > > Mark > Thanks a lot
Sebastian -- 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