AMBER Archive (2003)

Subject: Re: Velocity

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Feb 17 2003 - 12:02:34 CST

this information is not stored unless you wrote
a velocity file with ntwv>0. The restart
file has velocities for the last snapshot only.
If you saved multiple restart files, then you
have velocities at those times.
The coordinates in your trajectory file
are almost certainly too far apart in time
to use a finite difference to estimate velocities.
Carlos

----- Original Message -----
From: "A. Hungie" <hungie01_at_hotmail.com>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Monday, February 17, 2003 11:01 AM
Subject: Velocity

> Dear All,
>
> I have done MD simulations of DNA. In my trajectory file, there were only
> coordinates of all atoms and box size, no velocity. Could anyone tell me
how
> I can calculate velocity of any atom? I would like to know, for example,
> velocity of atom N9 of residue 4 at the time 200th ps. I don't want to
> re-run the production to store coordinates and velocities.
> Thank you very much in advance.
>
> Hungie
>
>
>
>
>
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