Re: [AMBER] What can we do with velocities file ?

From: Jason Swails <>
Date: Mon, 6 Dec 2010 21:31:46 -0500

Momentum coordinates are 3N of the 6N dimensions of phase space. Having the
masses in the prmtop file, the velocity file allows you to characterize that
part of phase space. However, classical statistical mechanics states that
the potential energy is dependent only on the coordinates while the kinetic
energy is only dependent on the momenta.

I can imagine there are uses for the velocities, but since they're fairly
expensive to dump to a file and not often useful for the questions typically
asked, they're not printed out by default. Also, it gives you, coupled with
the coordinate trajectory file, the ability to restart the simulation from
an arbitrary point in the simulation.

There may also be questions people wish to ask about velocity distributions
(i.e. verify that a target velocity distribution is actually achieved, etc.)

Perhaps others can suggest more uses.

Hope this helps,

On Mon, Dec 6, 2010 at 9:03 PM, setyanto md <> wrote:

> Dear amber user and developer
> After make production run, I got velocities (mdvel) file beside trajectori
> file (mdcrd). What Information can we got from velocities file ?
> as far as i know, I used velocities file to get Maxwel-distribution. Is
> there anything else ?
> Thank you for your attention
> setyanto
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Dec 06 2010 - 19:00:02 PST
Custom Search