[gmx-users] Correcting PBC effects

Siew Wen Leong ariel.leongsw at gmail.com
Tue Feb 21 10:33:31 CET 2012

Dear all,

Have anyone tried using CHARMM36 equilibrated POPE bilayer by Dr.Klauda

I am planning to use the membrane patch for a transmembrane protein
simulation. At first visualization, the membrane patch consists of a
bilayer with a single layer of water and then several lipids sticking out
from the opposite side of the water. So I presumed that to be an effect of

How can I correct this in Gromacs?

I've generated a .tpr for the system to use trjconv to manipulate the PBC

Out of all the combinations of pbc treatments, this one works:

trjconv -f pope80-c36box.gro -o pope80_pbc10.gro -s pope80.tpr -pbc mol

This puts the center of mass of the molecules in the box so I got a lipid
bilayer with a single, thick layer of water.
then followed by

trjconv -f pope80_pbc10.gro -o pope80_pbc11.gro -s pope80.tpr -pbc mol

to center the membrane on POPE.

The result looks fine (a hydrated bilayer) but I'm a new user to Gromacs so
I just wanted to ask if the workflow is reasonable.

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