[gmx-users] Adding detergent to simulation box

[Yasser Almeida Hernández]

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