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

Mark Abraham mark.j.abraham at gmail.com
Thu Mar 23 15:37:42 CET 2017


I can't comment on the appropriateness of your protocol, but to implement
it, take your solute and use editconf to rotate it so your intended vector
so it aligns with an appropriate axis, and put e.g. a suitable rectilinear
box on that before filling it with solvent.


On Thu, Mar 23, 2017 at 3:25 PM Chalaoux, Francois-Regis <
Francois-Regis.Chalaoux at evotec.com> wrote:

> 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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