[gmx-users] PBC problem in bilayer system

shahab shariati shahab.shariati at gmail.com
Thu Sep 11 13:10:42 CEST 2014

Dear Gromacs users

Unfortunately, no one did not answer my previous question about
selection of appropriate option for trjconv -pbc to solve pbc problem.

For preparation of initial system, I inserted 4 drug molecules in
close vicinity to the membrane surface in water phase, in one side of

I obtained the Z coordinate (along the bilayer normal) of the center
of mass of the 4 drug molecules (violet, blue, red and green lines)
and DPPC lipid bilayer (black line) as a function of simulation time,
using g_traj tool.

The related figure is in following link:


Do this state is related to pbc problem?

How to solve this issue?

Any help will highly appreciated.

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