VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Wed Dec 20 2023 - 09:31:18 CST

Hi, Ananya.
Pathways is an external plugin. I checked their github, and right now,
there are no examples for us to test.
https://urldefense.com/v3/__https://github.com/balabin/pathways__;!!DZ3fjg!7BZoKQQc0vIWZFgepaWN28CB_aV3awdtN-RGkE16wSLTAp2iR6fyWYQZkOHGc4SEyi_kMxmCMoLzqCjBudaL$

About the VMD movie, my guess is that since you've got the "Zero
pathway found" there is nothing to create a movie for.

If you'd like to share a working example, and the one that fails I'd
be glad to help debugging.
I also contacted the developer, but it is the holiday season, so it
might take some time to get a response.

Friendly,
Diego.

On Thu, Dec 14, 2023 at 3:12 AM Ananya Nayak <ananyanayak_at_tifrh.res.in> wrote:
>
> Hi, I'm using the VMD pathways plugin for the first time. I'm analyzing a trajectory, these are few issues I'm facing while doing it. I'll be grateful for any insight.
>
> 1. When I'm giving the trajectory with PSF file with water in it, it shows the error " missing operator at _@_ in expression "7093 _@_17093+1". And I've three systems it's same for all of them; only the expression line number changes. But if I remove the hydrogen from water, there is no problem; it runs fine. Also, without water it runs fine. I've tried to give 'with h' and 'without h' in the command line; while without h it gives me the above missing operator error; with h it shows the "warning: pathcore shows errors, segmentation violation and child process killed for every frame. Zero pathways found".
> But I've tried the systems in all the above mentioned conditions even in vacuum too and I got some pathways. I'm unable to figure out what is the problem when I'm adding the Hydrogen of waters.
>
>
> 2. I'm running the VMD in text mode in a cluster which doesn't have a graphical interface, so after all the frames are analyzed it can't generate a movie and exits, the next step should be the fluctuation analysis, but it doesn't go there. Is there a way to do that? 

--
Diego Enry B. Gomes, PhD
Department of Physics at Auburn University &
NIH Center for Macromolecular Modeling and Visualization
Leach Science Center - Ste. 3182 - Auburn, AL
dgomes_at_auburn.edu