From: Mark Zottola (
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 and the next frame the z-coordinate is 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

Thanks for any advice.