[gmx-users] Velocity autocorrelation

Krzysztof Kuczera kkuczera at ku.edu
Thu Mar 29 18:37:47 CEST 2012

You probably need to save velocities at least every 10 fs;
look at your plot on a fine enough time scale  - say 0-1 ps range
probably running in NVE ensemble would help as well
Krzysztof Kuczera

On 3/29/12 10:42 AM, Ignacio Fernández Galván wrote:
> Dear all,
> I'm trying to estimate the correlation time for my system, for the purpose of selecting a number of uncorrelated configurations and setting a good value for nstxout.
> My systems are usually small molecules in molecular liquids (water, methanol, acetonitrile, cyclohexane...). As a first approach, I calculate the velocity autocorrelation function for the pure liquid (or for a group containing only the solvent in a simulation of the full system).
> I expect to find a function more or less like the one shown here:<http://www.compsoc.man.ac.uk/~lucky/Democritus/Theory/vaf.html>. But instead I get a line that rapidly oscillates around 0, with an amplitude that progressively vanishes. I think I understand this behaviour, as it would be due to intramolecular vibrations or librations, but I don't find samples of this in the literature.
> My question is how can analyze this and extract some correlation time? How could I get some smooth function like the one shown in the above link? Am I doing something wrong? Is there another way to estimate a good value for nstxout?
> Any help or pointers to where to find it would be appreciated.
> Thank you,
> Ignacio

Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu

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