VMD-L Mailing List

From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Sun Sep 20 2020 - 17:21:56 CDT

Try unwrapping your coordinates prior to extracting them.

~ Bassam

On Sun, Sep 20, 2020 at 1:37 AM Mark Zottola <mzottola_at_gmail.com> wrote:

> 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.
>