VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Aug 25 2022 - 17:45:01 CDT

On Thu, Aug 25, 2022 at 12:27 PM Efthymiou, Christos <
christos.dereschuk.20_at_ucl.ac.uk> wrote:

> Hi,
>
> I would like to calculate the radius of gyration over the course of my
> NAMD simulation. I came across a paper discussing the DisRG plugin which
> can be used to calculate the radius of gyration. However, the link provided
> in the paper is broken and I cannot find any other sites with the code for
> this plugin. Does anyone have a link to the code so that I can install this
> plugin?
>
> If not, is there a script that can be used? I found a script on the VMD
> website for a PDB file, but I cannot find one to loop over the trajectory.
>

there should be an example in the VMD user's guide for how you can loop
over a trajectory. Now all you would have to do is to adapt that for use
with the "measure rgyr" command.
I am certain that the plugin you are looking for is doing something very
similar, but just gets some of the script parameters from a GUI (like so
many other VMD plugins with a GUI do).

axel.

>
> Thank you!
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!6SCQ8NeskVxvRkO6MiaeS4HoaglU3OrWCRuK9dUh4WYtACFPgceWh2PfQyypHTSWlirs8vvXvN50MFw_UQ$  
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.