From: Christopher Neale (
Date: Thu Sep 14 2017 - 22:34:52 CDT

This isn't an answer to the exact question you asked, but since you said trajectories, plural, the most efficient way to parallelize may be to run many concurrent VMD analyses in serial (if you have more trajectories than cores).

From: <> on behalf of Monika Madhavi <>
Sent: 14 September 2017 21:20:43
Subject: vmd-l: parallel processing in vmd

Hi all,

I used to write sequential tcl codes to analyze my MD trajectories with VMD. However, I would like to speed up my code and need to make it able to run in parallel. I am totally new to parallel computing and therefore I would like to have a very simple guide on how to do a small analysis in parallel.

For example, if I want to calculate the distance between (say) two atoms in every frame and write it into an output file, is it possible for vmd to process few frames at one time and wait till all frames are finished before writing the output? What would be the format of a sample tcl code for such a task?

Thank you.
Best regards,

W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.