Some good news … The tpr files provided by Simone do NOT show abnormal behaviour! This good news :))
However after turning ON the particle decomposition option to mdrun (-pd) I got a warnings of water not being able to be settled and a crash. This was still with Simone's trips … I took that as a good sign! Then I went back to my system and changed the topology to be able to turn OFF the particle decomposition that I need to use due to a "long" bond … the system when right trough 650 ps with many exchanges without a complain. I would have to check the continuity in the energies, Temp and other but it seems to be quite clear: The problem I am facing is located in the particle decomposition section of the code. I will fill a redmine and let see how to proceed from there. I won't be able to do this before middle of next week though. Tks for your help, XAvier. On May 2, 2013, at 2:36 PM, Michael Shirts <mrshi...@gmail.com> wrote: > Both. So if 4.6.1 doesn't work, I want to know so we can patch it > before 4.6.2 comes out. If it does work, then there is probably stuff > that can be backported. > > On Thu, May 2, 2013 at 8:32 AM, XAvier Periole <x.peri...@rug.nl> wrote: >> >> You mean working with or working on the code? >> >> I'll try gmx-4.6.1 >> >> On May 2, 2013, at 2:26 PM, Michael Shirts <mrshi...@gmail.com> wrote: >> >>> Quick check here -- is 4.6 behaving correctly? I actually spent some >>> time working on REMD in 4.6, and it seems to be behaving correctly in >>> my hands with temperature and pressure control. >>> >>> Thanks for any additional info on this! >>> >>> On Thu, May 2, 2013 at 8:18 AM, Mark Abraham <mark.j.abra...@gmail.com> >>> wrote: >>>> On Thu, May 2, 2013 at 12:58 PM, XAvier Periole <x.peri...@rug.nl> wrote: >>>> >>>>> >>>>> I saw that redmine report, which could be related but it seems to happen >>>>> only for runs done outside the domain and particle decompositions. >>>>> >>>>> I'll fill up a red mine. >>>>> >>>>> Anything I could do to help speeding the fix? >>>>> >>>> >>>> What'd be really nice is some thought on how one can demonstrate that the >>>> implementation of the exchange matches what would be expected from the >>>> theory. For T-exchange under NVT, it is sufficient to rescale velocities >>>> and quantities derived from them by the correct factor. That includes >>>> various things like T-coupling history and integrator half-step quantities >>>> (and does REMD with leap-frog make sense anyway?). For NPT, there's >>>> probably also some P-coupling quantities to scale, and the box to exchange. >>>> Anything I've missed? Hopefully virial contributions don't matter either >>>> way? >>>> >>>> Perhaps a decent first step is to hack the code to do a "self exchange," by >>>> clearing the entire state and rebuilding with what would/should be received >>>> from an exchange with a hypothethetical replica in an identical >>>> pre-exchange state. Only if the code can do that (i.e. mdrun -reprod >>>> produces a trajectory indistinguishable from a run that does not attempt >>>> this self exchange) is it worth considering proper state exchanges, and the >>>> process of making the code do the former should illustrate what is required >>>> for the latter. >>>> >>>> Mark >>>> -- >>>> 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 > -- > 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