[gmx-users] calculating com-com distances.

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Apr 13 09:43:41 CEST 2009

Hi Fernando,

> I've obtained the vectors for the rectangular box in g_energy,
> using Box_XX, Box_YY and Box_ZZ options; I didn't use the vectors of the
> skewed box.)

You have to use the three vectors from the tricilinic representation
to obtain the correct distance in the periodic system. Check PBC in
Chapter 3 of the manual.



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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