Hi, What David said, plus check out http://www.gromacs.org/Documentation/Terminology/Reproducibility
Mark On Thu, Jun 11, 2015 at 7:59 AM David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 11/06/15 03:59, 范聪 wrote: > > Hello, everyone! > > I've run two molecular dynamics using gromacs with exactly the same > inputs, in the very same computer, and there's no radom process such as > velocity distribution.( I've used "mdrun -t nvt.cpt" to stop a new velocity > distribution) > > Now I'm puzzled that gromacs have output two results of great > differences, both in the trajectory and in the energy calculation results. > Now I don't know which one to trust. > > I've learned that Molecular Dynamics software solve Newton equitations > to decide the movement of atoms, and calculate the potential energy > according to the location of each atom. > > So how could it happen that the very same inputs generate so different > results? > > Could there be some way to avoid all above? > > The simulations are still stochastic to some extent due to > parallellization and dynamic load balancing which is dependent on timing > the routines. There is a flag to maximize reproducability of the > simulation (mdrun -reprod IIRC) but it is probably not needed. > > You say nothing about the system and about the difference in energy. If > the systems are in equilibrium the average energies should be the same > in both simulations, within error bars of course. > > > > > > > > > > > > > > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > 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.