VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed May 23 2018 - 10:55:36 CDT

On Wed, May 23, 2018 at 11:28 AM, Nick Palmer <tuf90798_at_temple.edu> wrote:

> Hello,
>
> I am fairly new to VMD and NAMD and I was wondering if it was possible to
> get the kinetic energy or the velocity of a group of residues, say an alpha
> helix, at every frame of a simulation. I have tried writing the velocities
> for each individual atom of the structure every frame with {vx vy vz} which
> only outputted values of 0, and recently tried getting the velocity of the
> whole structure by measuring the center and getting the velocity out of
> that, which did not work as well. I am a bit lost and any help would be
> much appreciated. Thank you very much!
>

​nick,

dcd format trajectories that NAMD writes only contain coordinates, no
velocities. you have to explicitly request a velocity dcd file to record
velocities as well. i think you have to then load the velocities as
coordinates and use VMD/Tcl scripting to copy​ those over to the existing
trajectory file into the velocity fields. please google through the VMD
archives and i am certain you will find a post describing the process in
detail.

axel.

>
>
> --
> Nicholas J. Palmer
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.