Thanks for reply.
In my simulation I have saved trajectory at every 100 psec and time step of
simulation is 2 fsec. So should I need to save trajectory at every 10-20
fsec???
On Jun 7, 2017 7:06 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> George is right, and this information is in fact in the cpptraj
> section of the Amber 17 manual (page 645):
>
> "[usevelocity] Use velocity information in frame if present. This will
> only give sensible results if the velocities are recorded close to the
> order of the simulation time step."
>
> -Dan
>
> On Wed, Jun 7, 2017 at 9:13 AM, George Giambasu <giambasu.gmail.com>
> wrote:
> > Your plot seems to capture only the long time behavior of the velocity
> autocorrelation function (VAC). Water velocities de-correlate pretty
> quickly: probably on ~10-50 fs time intervals and to get the full details
> of the VAC you want o write the velocities with a higher frequency (few fs).
> >
> > George
> >
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>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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Received on Wed Jun 07 2017 - 10:00:03 PDT
