[gmx-users] why gromacs cannot repeat out the results?

[Mark Abraham]

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 <spoel at 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.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
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