[gmx-users] Box dimensions variation

[Tsjerk Wassenaar]

Hi Yasser,

Probably you're using semi-isotropic pressure coupling, which you should
only do if you have a membrane like structure aligned with the XY plane (or
a somewhat stiffish wire like structure aligned along z).

Cheers,

Tsjerk

On Wed, Aug 10, 2016 at 3:52 PM, Yasser Almeida Hernández <
yasser.almeida.hernandez at chemie.uni-hamburg.de> wrote:

> Hi all,
> I have a coarse grained system (membrane protein/water/ions/polymer) in a
> 20 nm box, running during 2 us. During the run the box dimensions varies
> significantly, increasing in Z and decreasing in X and Y (identically) to
> almost the same XY dimensions of my protein.
>
> Any ideas?
>
> Thanks in advance
>
> --
> Yasser Almeida Hernández
> PhD student
> Institute of Biochemistry and Molecular Biology
> Department of Chemistry
> University of Hamburg
> Martin-Luther-King-Platz 6
> 20146 Hamburg
> Germany
> +49 40 42838 2845
> yasser.almeida.hernandez at chemie.uni-hamburg.de
> office: Grindelallee 117, room 250c
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.