On 30/03/2012 2:42 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?
Manual 3.4.11 and 8.5 has some things to say.
Mark
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