VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 08 2014 - 10:08:18 CDT

Dominik,
  Yes, the "physical_time" field is supported by the molinfo command.
You will do better to refer to the current VMD documentation rather
than the very old VMD 1.7 user's guide that you had linked to below.
If you're using VMD 1.7 (that would be a shock), then you had best
upgrade to a current version! :-)

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu
 
On Sat, Sep 06, 2014 at 08:36:43AM +0200, Dominik Bottländer wrote:
> Dear Axel, Dear John, Dear Eddi,
>
> Thank you so much for your quick reply to my request and
> the helpful information you provided!
>
> @ Eduard Schreiner: You advised me of the true reason for
> the missing physical time information in VMD by confirming
> my assumption that the DCD file format does not contain
> the physical instants of time of the simulation.
>
> @ Axel Kohlmeyer: I actually wrote my own tcl-script to
> calculate the RMSD at the different frames of the
> respective trajectory to get some experience with
> tcl-programming in VMD and to specifically implement the
> position based RMSD definition in accordance with the
> GROMACS tool "gmx rms"
> (ftp://ftp.gromacs.org/pub/manual/manual-5.0.1.pdf#section.8.9).
>
> @ John Stone: Is "physical_time" a prescribed additional
> keyword of the "molinfo"-command
> (http://www.ks.uiuc.edu/Research/vmd/vmd-1.7/ug/node125.html)
> referring to the physical time field or is it possible to
> specify additional keywords of arbitrary names for the
> "molinfo"-command in order to store the physical time
> field or other data?
>
> Thank you very much for your answers in advance!
>
> With kind regards,
>
> Dominik Bottländer 

-- 
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/