lipid centering

From: Mihaela Drenscko (
Date: Tue Apr 11 2017 - 13:08:24 CDT


At the beginning of simulation I had solvated POPC, with POPC between two
water layers. Occasionally I've got water in the center and POPC above and
below water. I tried to center POPC using:

pbc wrap -center com -centersel "resname POPC" -all
pbc join fragment -all
pbc join fragment -bondlist -all

Positioning of POPC and water remain unchanged. What do you suggest I do
for centering?

Thank you very much,

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