VMD-L Mailing List

From: Mark Zottola (mzottola_at_gmail.com)
Date: Sun Sep 20 2020 - 02:01:08 CDT

I am tracking the path of ions in an MD simulation. I used VMD to extract
the coordinates from each frame and write it out to a PDB file.

I have run into a problem where suddenly one coordinate (usually y or z)
suddenly flips sign. In other words in one frame the z-coordinate would be
-15.xxx and the next frame the z-coordinate is +16.xxx. The other
coordinates remain close in value and identical in sign to the previous
coordinates. This continues for an indeterminate number of steps then the
offending coordinate flips back again.

I am surmising this has something to do with crossing over a boundary as we
are using periodic boundary conditions. Is there any way to obviate this
issue?

Thanks for any advice.