VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Mon Aug 12 2024 - 09:42:09 CDT

Hi Ryan,

You need to set the PBC box dimensions somehow. Most of the time in a trajectory, these come from the trajectory file itself, and this all happens transparently. You can see these dimensions with `pbc get -all` to see the box dimensions for all loaded frames. If it is only a few frames where the box is weird/nonsense, you can probably use `pbc set`with the appropriate arguments to correctly set the box dimensions in VMD (see https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/). Side lengths of zero and infinity are clearly signs that something is not right in the trajectory (or potentially in the file reader).

-Josh

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Ryan Woltz <rlwoltz_at_ucdavis.edu>
Date: Friday, August 9, 2024 at 8:15 PM
To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: pbc box unwrapping/wrapping error infinite bond angles/box sides

Dear community,

        I'm having an issue that I can't really find a good solution to. I've tried qwrap pbc tools and I've seen something about mdanalysis fixing this issue but just can't the examples are not for the nc and parm7 files I have so I'm not sure how to use it. I'm pretty sure I fixed this issue 2 years ago using some pbctools commands but I can't remember how. It might have been a pbc join command but the way I'm using it doesn't work like I'd like them to. I'm also on a publishing deadline so I don't have much more time to troubleshoot and was hoping someone can help with pbc join or some other command in vmd.

           The issue is for a few frames in my simulations the bond angles are infinite and one of the box sides in infinite. This makes pbc tool crash at that frame with this error:

vmd > pbc unwrap -all -sel "protein"
Info) 0.2% complete (frame 1)
ERROR) Suspicious pbc side length (a=0.000000 b=-inf c=-0.000000). Have you forgotten to set the pbc parameters?
ERROR) Suspicious pbc angle (alpha=363384373248.000000 beta=inf gamma=inf).
domain error: argument not in valid range

      I think the solution is in pbc join or pbc box but I do not have enough experience or confidence to know how to use these commands.

       Can someone help guide me to a page or suggest a command to define the box with proper dimensions for the bad frames or another way to process, maybe with mdanalysis?

Thank you,

Ryan