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

Vivien WALTER walter.vivien at gmail.com
Thu Feb 8 15:01:03 CET 2018

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/
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,

Dr. Vivien WALTER
Institut Charles Sadron
23, Rue du Loess
BP 84047
67034 STRASBOURG CEDEX 2, France
tel: +33(0)388 414 113
fax: +33(0)388 414 099

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