[gmx-users] about truncated octahedral periodic box

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jul 3 15:11:53 CEST 2007

Hi Yang Ye,

It was a different question; the question Rui Li asked was "why is my
protein not in the center of my truncated octahedron"?.

The answer to that question is not:
> You shall use trjconv -ur compact -pbc atom to transform your model.
but is more fundamentally related to understanding the principles of
periodic boundary conditions (rather than to the use of trjconv).

> This is my second time in the week answering this question.
I know.., I get the same feeling now and then.., but keep keen on
reading the question asked.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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