[gmx-users] Simulations of proteins in membrane bilayer
grx1985 at qq.com
Wed Sep 30 22:48:41 CEST 2015
I am doing a simulation in which a protein is inserted into a bilayer. In my simulations, the protein moved on the x-y plane of the bilayer (which is normal). However, in order to do some analysis, I have to put the protein to the center of the box, but still keep the box filled by lipids. Does anyone know how to do this?
Of course, I could put the protein to the center of the box by align the protein with that in the first snapshot, but in this way, some of the lipids will be out of the PBC box. In my case, I have to keep all of the lipids in the PBC box and packed around the protein.
I am really appreciate for your suggestions and help.
With my best regards,
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