From: Axel Kohlmeyer (
Date: Sun Sep 20 2020 - 21:12:41 CDT

On Sun, Sep 20, 2020 at 9:41 PM Mark Zottola <> wrote:

> I was told the coordinate files given to me were generated from a psf and
> dcd files extracted using the "Save Coordinates" command in VMD. I
> received a copy of these files and tried to extract them myself. I do not
> see where there is an option to "unwrap".
> Can you be a bit more explicit with your guidance?
> Thanks.
> On Mon, Sep 21, 2020 at 7:22 AM Bassam Haddad <> wrote:
>> Try unwrapping your coordinates prior to extracting them.
>> ~ Bassam
>> On Sun, Sep 20, 2020 at 1:37 AM Mark Zottola <> 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
>>> 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 issue?
>>> Thanks for any advice.

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.