VMD-L Mailing List
From: Ryan Woltz (rlwoltz_at_ucdavis.edu)
Date: Fri Aug 09 2024 - 17:58:42 CDT
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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
- Next message: Vermaas, Josh: "Re: pbc box unwrapping/wrapping error infinite bond angles/box sides"
- Previous message: Diego Gomes: "Re: CHGCAR file read in VMD"
- Next in thread: Vermaas, Josh: "Re: pbc box unwrapping/wrapping error infinite bond angles/box sides"
- Reply: Vermaas, Josh: "Re: pbc box unwrapping/wrapping error infinite bond angles/box sides"
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