From: Peter Freddolino (
Date: Sat Sep 26 2020 - 21:29:29 CDT

Try doing
package require pbctools

On Sat, Sep 26, 2020 at 6:49 AM Mark Zottola <> wrote:

> 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 <>
> wrote:
>> 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.