VMD-L Mailing List

From: Dominik Bottländer (bottlaen_at_rhrk.uni-kl.de)
Date: Thu Sep 04 2014 - 10:12:22 CDT

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 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.

I appreciate any information in this matter!

With kind regards,

Dominik Bottländer (Bottlaender)