[gmx-users] Velocity autocorrelation

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 30 19:46:04 CEST 2012

On 2012-03-30 19:39, Ignacio Fernández Galván wrote:
> --- On Fri, 30/3/12, David van der Spoel<spoel at xray.bmc.uu.se>  wrote:
>>> 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?
> Nothing special. I built an OPLS-AA topology with 5 bonds, 7 angles, 3 dihedral and 3 pairs (<http://djelibeibi.unex.es/files/ACN.itp>). Visual inspection of the conformations shows an almost linear CN group in every molecule, and g_angle gives an average of 177, and a distribution that looks fine to me.
>>>> 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.
>> From g_msd I get a D of around 5.6e-5 cm^2/s which looks about the right order of magnitude? (Default OPLS-AA acetonitrile is not very good, anyway.) Integrating the VACF gives 4.8e-5 cm^2/s
> Perhaps I should try with a larger system / longer simulation?
> I can provide all the input files if needed.

No need, I think it is just fine!
What your seeing is the average vacf per atom, and apparently there are 
correlations between the vibrations which cause the oscillation. In 
theory both VACF should be the same but they are relatively close. A 
longer simulation is always good of course.
> Thanks,
> 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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