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