VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 04 2014 - 11:10:30 CDT
One minor correction to Axel's reply:
VMD does have a "physical time" field, but the majority of trajectory
file formats and associated readers do not implement this feature, so
while VMD does actually store this information when available, for all
practical purposes Axel's statement is still correct. If you have the
physical time associated with a timestep, you can set this value in VMD
via the Tcl scripting interface, and it will be associated with the
other per-timestep data VMD stores. You can show the physical_time
in VMD labels, set/get this info using "molinfo top get physical_time",
and similarly for Python, etc.
On Thu, Sep 04, 2014 at 05:51:44PM +0200, Axel Kohlmeyer wrote:
> On Thu, Sep 4, 2014 at 5:12 PM, Dominik Bottländer
> <bottlaen_at_rhrk.uni-kl.de> 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 akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/