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?
Thank You
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