VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Sep 08 2014 - 12:45:34 CDT

dominik,

On Mon, Sep 8, 2014 at 1:07 PM, Dominik Bottländer
<bottlaen_at_rhrk.uni-kl.de> wrote:
> 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.

since you are using LAMMPS, would you be willing to change to a
different file format for your work?
and make some tests and help with improving this format to import this
information natively into VMD?

LAMMPS supports a variety of formats (either directly or through an
interface to VMD's molfile plugin library. i would have to discuss
with other developers, whether an extension to the native file formats
can be done or whether it would only be possible through the molfile
plugins. this discussion reminded me of some inquiries on the LAMMPS
mailing list, where users that use variable time steps, were looking
for a way to have an (approximately) even spacing between frames in
time and not time steps.

so there is an opportunity to add some real value to both LAMMPS and VMD.

axel.

>
> 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!
>
> Dominik
>
>
> 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
>> 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
>
> 

-- 
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.