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 - 07:00:02 PDT
