[gmx-users] Re: Membrane Simulation

Giuseppe giuseppe.cimicata at studenti.unito.it
Fri Apr 19 13:37:31 CEST 2013

Dear Justin, 

thank you very much for replying. When I run the editconf tool I set for
sure the right box vectors (6.23910   6.17970   6.91950) so that in the
system.gro file (according to the nomenclature of your tutorial) the box
vectors from the protein structure and from the membrane are the same, but i
noticed that, after using the perl tool, they magically changed (e.g. in the
system_inflated.gro file they became 24.95640  24.71880   6.91950). Maybe
something is wrong with the "-center" option? I include the complete
editconf command that I run: "editconf -f protein_processed.gro -o
protein_newbox.gro -c -box 6.23910   6.17970   6.91950 -rotate 85 -10 55
-center 8 8 6". Thanks for your patience and your appreciated help.

Yours sincerely,  


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