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

[Chalaoux, Francois-Regis]

Hi All and thank you Mark for your answer,

I created a vector with make_ndx between 2 atoms but I can't find how to use this vector with the editconf command. The "rotate" option needs for a vector representing the rotation around axis Z ( 0 , 0 , 60) but the result seems not to be of this amplitude. At startup, the choice with editconf seems not to give the possibility to choose my vector, only the system size (I chose my vector) and the group for output (I chose system).

gmx editconf -f complex.gro -o newbow.gro -bt cubic -n index_vect1.ndx -d 1.0 -rotate 0 0 60

Any idea ?

FR.

-----Message d'origine-----
De : gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] De la part de Mark Abraham
Envoyé : jeudi 23 mars 2017 15:37
À : gmx-users at gromacs.org
Objet : Re: [gmx-users] Align a vector with an axis of the box

Hi,

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.

Mark

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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