From: Giacomo Fiorin (
Date: Tue Oct 03 2017 - 15:18:34 CDT

Hi Mo, manipulating coordinates is usually done by creating atom selections
and using commands with the Tcl scripting language. Check the VMD user
guide for the syntax, and the script library for some examples.


On Tue, Oct 3, 2017 at 9:29 AM, Mo Rahman <> wrote:

> Hello,
> After analysing the output of an MD simulation, I have obtained the
> frequencies of the vibrational modes of the system as well the Cartesian
> components of the force and torque vectors for each heavy atom.
> Given this information, in particular the force and torque data, is there
> a way for me to use VMD to create an animation of each of the vibrational
> modes? I'm only familiar with the basic functionality of the software and I
> have no idea where to begin.
> Thanks in advance!
> Mo

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD