VMD-L Mailing List

From: Josh (vermaasj_at_msu.edu)
Date: Mon Oct 16 2023 - 08:54:23 CDT

Hi Raman,

It might be possible with some tkcallbacks or something to check if the
file modification date changes, and then automate the usual loop of
deleting the existing coordinates with the animate command, and then
loading new coordinates with the animate command.
(https://www.ks.uiuc.edu/Research/vmd/current/ug/node121.html)

In terms of the .itp or .top file, there are scripts floating around the
web to do this. Another option if you have the super bleeding edge VMD
installed from source is to use the file reader plugin for .tpr files
that was recently added to the VMD source tree, derived from what is on
github (https://urldefense.com/v3/__https://github.com/jvermaas/vmd-tprreader__;!!DZ3fjg!7lt48aYQZOsKQ9v0QsvYTsHEwTM2jeSJn8G5WGkjX3EFuQv3MZu2lJBFMqLvV0g7OCBt4s8rJ7cEEW_JDLI$ ). As it stands right
now, that functionality is in CVS, but not in any of the releases on the
download page.

-Josh

On 10/16/23 3:18 AM, Raman Preet Singh wrote:
> Dear VMD Users,
>
> I am developing a script to generate Gromacs input files (.gro and
> .itp) for a large structure. This involves testing the output files
> for accuracy.
>
> Let's say the default filename that the script generates is
> structure.gro. When I load structure.gro file, the atom positions can
> be seen. When I make any corrections to the script or generate the
> structure with a different set of parameters, a new structure.gro is
> generated and replaces the previous structure.gro file. However, the
> previous structure remains loaded in VMD and I have to manually delete
> the loaded structure and then load the new structure.gro file. Since
> the filenames are the same, is it possible to dynamically update the
> structure in VMD so I can have a look after every change is made in
> the script or in the input parameters and avoid the load-delete-load
> cycle.
>
> A related question is: is there an easy way to load Gromacs itp or top
> file for bond information much like VMD reads from a psf file?
>
> Thanks,
> Raman
>
>
>
>
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-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io