[gmx-users] Membrane Simulation

Giuseppe giuseppe.cimicata at studenti.unito.it
Thu Apr 18 16:59:46 CEST 2013

Dear all
I'm trying to start a simulation with a protein embedded in a bilayer of
POPC molecules, but I have some problems when I pack the lipids around the
protein. Infact I place the protein in the proper position using the
editconf tool with the “-rotate” and “-center” options on, but when I scale
the lipid positions with the perl script (before the energy minimization),
the protein moves up, de facto off from the membrane! Obviously I've set
very strong position-restraining force on protein, but it moves the same.
Probably the problem is trivial, but I can't see it, so any help is much
Thanks a lot,
GIuseppe Cimicata

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