Dear all, Have anyone tried using CHARMM36 equilibrated POPE bilayer by Dr.Klauda http://terpconnect.umd.edu/~jbklauda/research/download.html?
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 PBC. How can I correct this in Gromacs? I've generated a .tpr for the system to use trjconv to manipulate the PBC box. 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 -center 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. -- Regards, Ariel.
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