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

[Vivien WALTER]

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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