Thanks for the answer. I'll check gmx4.5.7 and report back. I am not sure what you mean by GROMACS swaps the coordinates not the ensemble data. The coupling to P and T and not exchanged with it? That would explain what I see, but let see what 4.5.7 has to say first.
Tks. On Apr 25, 2013, at 22:40, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Thanks for the good report. There have been some known issues about the > timing of coupling stages with respect to various intervals between GROMACS > events for some algorithms. There are a lot of fixed problems in 4.5.7 that > are not specific to REMD, but I have a few lingering doubts about whether > we should be exchanging (scaled) coupling values along with the > coordinates. (Unlike most REMD implementations, GROMACS swaps the > coordinates, not the ensemble data.) If you can reproduce those kinds of > symptoms in 4.5.7 (whether or not they then crash) then there looks like > there may be a problem with the REMD implementation that is perhaps evident > only with the kind of large time step Martini takes? > > Mark > > > On Thu, Apr 25, 2013 at 1:28 PM, XAvier Periole <x.peri...@rug.nl> wrote: > >> >> Hi, >> >> I have been recently using the REMD code in gmx-407 and gmx-453 and got a >> few systems crashing for unclear reasons so far. The main tests I made are >> using gmx407 but it is all reproducible with gmx453. The crashing was also >> reproduced (not necessarily at the same time point) on several >> architectures. >> >> The system is made of a pair of proteins in a membrane patch and for which >> the relative orientation is controlled by non-native bond/angles/dihedrals >> to perform an umbrella sampling. I use the MARTINI force field but that >> might not be relevant here. >> >> The crashes occur following exchanges that do not seem to occur the >> correct way and preceded by pressure scaling warnings … indicative of a >> strong destabilisation of the system and eventual explosion. Some >> information seems to be exchanged inaccurately. >> >> Trying to nail down the problem I got stuck and may be some one can help. >> I placed a pdf file showing plots of bonded/nonbonded energies, >> temperatures, box size etc … around an exchange that does not lead to a >> crash (here: md.chem.rug.nl/~periole/remd-issue.pdf). I plotted stuff >> every step with the temperature colour coded as indicated in the first >> figure. >> >> From the figure it appears that the step right after the exchange there is >> a huge jump of Potential energy coming from the LJ(SR) part of it. Although >> there are some small discontinuities in the progression of the bond and >> angle energy around the exchange they seem to fine. The temperature and box >> size seem to respond to it a few step latter while the pressure seems to be >> affected right away but potentially as the Epot will affect the viral and >> thus the Pressure. >> >> The other potential clue is that the jumps reduce with the strength of the >> pressure coupling. A 1/2 ps tau_p (Berendsen) will lead to a crash while a >> 5/10/20 ps won't. Inspection of the time evolution of the Epot, box … >> indicates that the magnitude of the jumps is reduced and the system ca >> handle the problem. >> >> One additional info since I first posted the problem (delayed by the file >> first attached but now given with a link) the problem is accentuated when >> the replicas differ in conformation. I am looking at the actual differences >> as you'll read this email. >> >> That is as far as I could go. Any suggestion is welcome. >> >> XAvier. >> MD-Group / Univ. of Groningen >> The Netherlands-- >> 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 -- 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