[gmx-users] PBC in membrane protein system

Yasser Almeida Hernández yasser.almeida.hernandez at chemie.uni-hamburg.de
Tue Oct 6 14:22:09 CEST 2015

Hi all,

I am simulating a membrane protein in coarse-grained mode. The protein 
diffuse in the membrane and in the final frame my protein is in one of 
the box borders, so the coordinates are splitted to the opposite border 
(PBC). Then when I used backward.py to translate to all-atom 
coordinates, also results in splitted coordinates. I've tried several 
trjconv option with any success. How can I get the protein centered in 
the membrane?

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

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