[gmx-users] PBC problem in bilayer system

shahab shariati shahab.shariati at gmail.com
Mon Sep 15 10:59:36 CEST 2014

Dear Tsjerk

Thanks for your reply.

I think that there is another problem, except for visualization.

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:


 This Figure is not normal and usual.

 What is your opinion about this issue?

Best wishes,

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