VMD-L Mailing List

From: Olaf Lenz (olenz_at_icp.uni-stuttgart.de)
Date: Sun May 25 2014 - 05:41:59 CDT

What do you mean to "disable PBC" in your script? The PBC are in your
system.

If you monitor the distance of two molecules in PBC, you will want to
measure the "minimal image distance", i.e. the distance of a molecule to
the closest periodic image of another molecule.
When you simply measure the Euclidian distance of the molecules in the
central image, which is what you seem to have done, you will see jumps in
the distance.

What distance you really want to measure depends on the question you try to
answer.

Olaf

2014-05-24 4:30 GMT+02:00 Ozgun Kirker (Student) <okirker_at_sabanciuniv.edu>:

> Hello all,
>
> I am trying to measure the distance between 2 molecules through a
> trajectory, but because of PBC sometimes molecules warp around and I get
> spikes in my data.
> How can I disable PBC in my script?
>
> Thanks in advance.
> 

-- 
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607