[gmx-users] Adding detergent to simulation box - SOLVED

[Yasser Almeida Hernández]

I solved the problem adding NG, water and ions in that order.

Cheers

Yasser


On 10.01.2017 13:25, Yasser Almeida Hernández wrote:
> Hello all,
>
> I am trying to build a system containing a membrane protein, water, 
> ions and NG detergent (beta-nonylglucoside). A conflict arise when I 
> try to add NG and ions. If I build the system containing the protein, 
> water and ions, and then add NG (with -ci and -nmol options of genbox 
> command), none NG molecule is added. On the other hand if I build the 
> solvated box with the protein and NG, and then add the ions, the NG 
> molecules are destroyed/disordered and clustered in the box edges.
>
> Any thoughts?
>
> Thanks in advance
>
> Yasser
>

-- 
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