Hi Mark, Thank you for the quick answer. However, the problem is not only a problem of reproducibility of a single simulation. To make sure that I have converged results with proper sampling, I am performing each time 10 simulations of the same system with different positions of the solvent molecules and different initial velocities. For the 10 simulations, I had reached a plateau at 250ns for the parameters I am looking at. When extending to the GPU machine, for the 10 simulations I see these parameters increasing. For other sets of simulations with the same solute but different water:glycerol molar fractions, the plateau stays stable until 300ns and I never saw this kind of increase. That's why I was wondering if there is a big red flag when extending simulations on another machine or switching from CPU to GPU.
Thank you. Nicolas Le mar. 5 juin 2018 à 10:43, Mark Abraham <mark.j.abra...@gmail.com> a écrit : > Hi, > > You'll basically never get a reproducible trajectory > http://www.gromacs.org/Documentation/Terminology/Reproducibility. If your > conclusions would depend on the configurations in any single trajectory, > you'll have a hard time demonstrating that those conclusions are valid > reflection of reality. > > Mark > > On Tue, Jun 5, 2018 at 10:37 AM Nicolas Cheron < > nicolas.cheron.bou...@gmail.com> wrote: > > > Dear all, > > > > I ran a 250ns simulation with Gromacs 5.1.2 on a machine with only CPUs. > I > > then wanted to extend the simulation to 300ns, and copied the .tpr and > the > > .cpt to another machine with GPUs (also running Gromacs 5.1.2). I > observed > > strange results, so I decided to also extend the simulation (from 250ns) > on > > the first machine to compare. > > > > Different results are obtained for the 2 extensions (that were started > from > > the same .tpr and .cpt) on the 2 different machines/architectures. Is it > a > > known behaviour, and one should never proceed like this? Is it due to > > CPU/GPU, or only the fact that machines are different and the same would > > have happened on another CPU machine? > > > > Thank you > > > > Nicolas > > > > PS: I am looking at a solute in a water:glycerol mixture. By "different > > results" I mean that the number of water (or glycerol) around the solute > > are different at all time steps > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.