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