From: Dominik Bottländer (
Date: Mon Sep 08 2014 - 12:07:12 CDT

Hello John,

thank you for getting back to me about the "physical_time" field of the
molinfo command! I will definitely use the field to store the physical
instants of time of my simulations and to access them in my trajectory
analysis tcl-scripts.

Due to your hint I noticed that I had included a link to the VMD 1.7
User's Guide in my original post on this topic. That must indeed have
been a shock! :-) The link was my first search result when I quickly
looked up "vmd molinfo" on Google. I use VMD 1.9.1 and usually also
consult the pdf-version of the respective current User's Guide.

Have a great day!


Am 08.09.2014 17:08, schrieb John Stone:
> 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
> 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"
>> (
>> @ John Stone: Is "physical_time" a prescribed additional
>> keyword of the "molinfo"-command
>> (
>> 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