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

Yasser Almeida Hernández yasser.almeida.hernandez at chemie.uni-hamburg.de
Tue Jan 10 14:44:01 CET 2017

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



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
+49 40 42838 2845
yasser.almeida.hernandez at chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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