Re: Random Velocities Question

From: Axel Kohlmeyer (
Date: Tue Jul 03 2018 - 22:37:39 CDT

On Tue, Jul 3, 2018 at 11:11 PM McGuire, Kelly <> wrote:

> I've been told that NAMD has randomized velocities built in now. If you
> run a simulation, and then submit that simulation again, the velocities are
> automatically randomized, is that true? If so, how do I turn that off? I
> would like to run the same exact simulation again, but only change the
> partial charges on my ligand. If the velocities are randomized in the same
> simulation, then I won't know if the partial charges or the new velocities
> changed my results. I am looking to see how much the different partial
> charges has an effect on my results. Thanks!

i see a logic problem with this approach. what you describe would apply
only in a case, where you can assume a linear response regime​. however,
that doesn't apply for the case where the properties of your system is
described by a statistical mechanical ensemble, i.e. you need to average
over multiple configurations. here your perturbation is just a small random
change, that will cause a divergence simply because MD is a chaotic system.
that divergence (same as different randomized velocities) by itself has no
meaning, unless it is significant across an ensemble of independent

thus to be certain, that a (small) change has a consistent and
statistically significant impact on your system, you have to *use* the
divergence caused by randomization. i would in your situation create a
significant number of de-correlated snapshots of the same (original,
unperturbed) system, e.g. a collection of statistically independent frames
taken from a long equilibrium simulation and use those as starting points
for a collection of simulations with a perturbation. then i would look for
statistically significant differences when averaging over all those
simulations. only, if you can converge those results beyond the inherent
fluctuations and statistical uncertainties, you have proof, that your
change has a statistically significant effect.


> *Kelly L. McGuire*
> *PhD Scholar*
> *Department of Physiology and Developmental Biology*
> *Brigham Young University*
> *LSB 3050*
> *Provo, UT 84602*

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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