From: Axel Kohlmeyer (
Date: Thu Sep 04 2014 - 10:51:44 CDT

On Thu, Sep 4, 2014 at 5:12 PM, Dominik Bottländer
<> wrote:
> Dear users and developers of VMD,
> I am a relatively new user of VMD. For the molecular stability analysis of
> my molecular dynamics simulations with LAMMPS I wrote a simple tcl-script to
> calculate the RMSD at each frame relative to the first frame. The number of

while it is likely good practice to get some programming experience in
VMD scripting,
are you aware of this plugin that is shipped with VMD?

> frames in the respective simulation can easily be inquired by the "molinfo"
> command implemented in VMD ("molinfo $mol get numframes") which allows to
> specify a for-loop over all frames for the RMSD calculation. So far, my
> script writes the RMSD as a function of the frame index in an output file.
> However, I would like to display the RMSD as a discrete function of the
> actual simulation time for each frame. I have not found a way yet to obtain
> the actual simulation time for a frame in VMD.
> Therefore, I would like to know whether VMD provides the actual simulation
> time for each frame of a trajectory and in which way it can be accessed. Of
> course, as I know the timestep of the respective simulation I can calculate
> the actual simulation time for each frame via the "expr" tcl-command.
> Nevertheless, I am interested if the simulation time for each frame is
> directly available in VMD. My trajectory data are stored in and read in into
> VMD from dcd-files.

no. VMD does not hold that information.

> I appreciate any information in this matter!
> With kind regards,
> Dominik Bottländer (Bottlaender)

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.