[gmx-users] Velocity autocorrelation

Ignacio Fernández Galván jellby at yahoo.com
Fri Mar 30 19:39:07 CEST 2012

--- 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.


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