[gmx-users] Velocity autocorrelation

[David van der Spoel]

On 2012-03-30 12:41, Ignacio Fernández Galván wrote:
> --- On Thu, 29/3/12, Krzysztof Kuczera<kkuczera at ku.edu>  wrote:
>
>> 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
>
> Thanks for your suggestion. I was already saving velocities every 10 fs. I tried with a NVE ensemble, but the behaviour is the same.
>
> I have uploaded a sample velocity ACF here:
> http://djelibeibi.unex.es/files/vac_NVE.xvg
> That's the autocorrelation file for CN atoms in acetonitrile.
>
> I have also uploaded the corresponding mdp file:
> http://djelibeibi.unex.es/files/dinamica_NVE.mdp
>
> I still don't know how to properly analyze this, I would say that I want the amplitude to drop to almost zero, and that would mean a relaxation time of ~5-6 ps. But is this the correct/expected behaviour?
>
> Thank you,
> Ignacio
Why are you freezing part of the system?

The VAC looks ok doesn't it? How many molecules?

What is the temperature of your system?

Is it starting from an equilibrated liquid?
-- 
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