[gmx-users] Align a vector with an axis of the box

Chalaoux, Francois-Regis Francois-Regis.Chalaoux at evotec.com
Thu Mar 23 15:24:54 CET 2017

Hi All,

To realize an umbrella sampling of JZ4 in the Lyzosyme (3HTB) I have to define a box enough long to pull JZ4. I choose a reaction coordinate between Calpha THR109 and JZ4-COM.
Presently, this coordinate (vector) is not aligned with an axis of my cubic box and after a pulling should exceed the one-half of the final box and create an interaction with an image with PBC. So I would like to align this vector with an axis of the box. If my protocol makes sens , How to align this vector with an axis of the box ?

Cheers, FR.


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