From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Sep 20 2020 - 21:12:41 CDT

https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

On Sun, Sep 20, 2020 at 9:41 PM Mark Zottola <mzottola_at_gmail.com> 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 <bhaddad_at_pdx.edu> wrote:
>
>> 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.
>>>
>>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.