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: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
