AMBER Archive (2008)

Subject: Re: AMBER: velocity autocorrelation function for SPC felxible water model

From: David A. Case (
Date: Thu May 08 2008 - 17:54:57 CDT

On Thu, May 08, 2008, Rahaman, Asif wrote:
> Yes, I did include the frcmod.spcfw file while creating the topology and
> crd file. I do not understand why I get some wiggles at the bottom of the
> VAC function. Is it something inherent in AMBER SPC flexible water model or
> something is wrong with my simulations. Has the model been tested in terms
> of VAC?

I assume(?) you have looked at Fig. 2 of JCP 125:184507, 2006.

If you are sure that your simulations are converged, you might want to contact
Francesco Paesani to see if he has any comments or experience that is relevant
here. There could be something tricky in how the velocities are computed, I
suppose. The frequency of your wiggles seems way too slow to be related to
any internal motion. Have you tried running SPC (or SPC/E) itself?


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