[gmx-users] Centering the system

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed Oct 16 14:29:42 CEST 2013

Dear gmx users,

I have a system consist of a lipid bilayer and a peptide. As the initial configuration, the peptide is located in center of the x-y plane above lipid bilayer. After running MD, the peptide shows interactions with the polar groups. It's ok, but the peptide is near one edge of the x-y plane of the bilayer. I' d like to know if there is any way to use the properties of the pbc and see the peptide in center of the x-y  plane while interacting with the polar groups?

Thanks in advance,
Your suggestions would be appreciated.


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