From: Mark Zottola (mzottola_at_gmail.com)
Date: Fri Sep 25 2020 - 18:51:17 CDT

I have tried to access pbcunwrap in the pbctools2.8 to no avail. THere is
no extension pdbtools in the menu of VMD. Using the VMD command window and
going into the pbctools2.8 directory and issuing the command
./pbcunwrap -first now gives me the response "invalid command name". If I
leave off the ./ I get the same response. I uninstalled and
re-installed VMD (1.9.3 for Windows) in case something might have been
hosed. I get the same result. How do I access this plugin?

On Mon, Sep 21, 2020 at 11:12 AM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>