[gmx-users] Problem with Gromacs and Charmm force field dump rates

Mark Abraham mark.j.abraham at gmail.com
Thu Feb 8 15:13:53 CET 2018


One simulation at each dump rate doesn't lead to a reliable conclusion that
the change in volume may be related to the dump rate, because if you run
replicates at each dump rate, they would not reproduce each other. If you
run such replicates and there is, or is not, a consistent trend, then that
can suggest the presence (respectively, absence) of a connection between
volume change and dump rate.


On Thu, Feb 8, 2018 at 3:01 PM Vivien WALTER <walter.vivien at gmail.com>

> Hi Peter,
> Thank you for the swift reply. Here are some details about your answers. I
> hope the problem will appear more clear with them.
> > Increase/decrease by how much? Is it converged?
> The results completely diverge, that is the problem. The interactions we
> are observing through the simulations are in opposition: attraction with
> high dump rates (25000 steps) or repulsion with low dump rates (2500
> steps), hence the change in box size. This is why we are confused about
> these simulations.
> > Don't do this (http://www.gromacs.org/Documentation/Terminology/
> Thermostats)
> We use two coupling groups: one for the sugar molecules and the solvent
> (water), and the one for a macromolecule interacting with the sugar.
> > Simulations perfomed by Gromacs are not binary reproducible, so you will
> > (never) get exactly the same result twice starting from the same point.
> > This is inherent in how the simulation is performed.
> > http://www.gromacs.org/Documentation/Terminology/Reproducibility
> > This is why sampling is so important, to show that the fluctuations you
> > see average out and are not depending on stochastic errors or the
> > starting conformation.
> Similar answer than in the first point: the problem are not the
> fluctuations between measurements leading to the same average result, but
> the complete divergence between the behiavors at low and high dump rates.
> Best regards,
> Vivien
> --
> Dr. Vivien WALTER
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