[gmx-users] Velocity autocorrelation

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 30 17:51:12 CEST 2012

On 2012-03-30 13:15, Ignacio Fernández Galván wrote:
> --- On Fri, 30/3/12, David van der Spoel<spoel at xray.bmc.uu.se>  wrote:
>> Why are you freezing part of the system?
> I want a given molecule (20 atoms) to be rigid. Is there a better way that works for any kind of molecule (not just water)? I believe freezing it should be equivalent to keeping it rigid and removing the center of mass motion.
>> The VAC looks ok doesn't it? How many molecules?
> My concern is it doesn't look like the typical VAC I find in the literature (as in<http://www.compsoc.man.ac.uk/~lucky/Democritus/Theory/vaf.html>), and I don't know how to quantitatively analyze this function.
It looks like it is relaxing slowly from an unnatural conformation / phase.

> There are 459 solvent (acetonitrile) molecules. Not too many, I know, but it's box size of ~40 Å.
And how are you treating the linear angle?
>> What is the temperature of your system?
> Around 295 K.
>> Is it starting from an equilibrated liquid?
> Yes, or so I believe. I run a 50 ps equilibration first, and use the resulting checkpoint with -t
Have you checked the diffusion constant to test whether it is liquid?
You can do that from the VACF and from the mean square displacement.
> Thank you,
> Ignacio

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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