[gmx-users] PBC problem in bilayer system

[shahab shariati]

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:



https://www.dropbox.com/s/op8gaxeto4z7qxq/figure.TIF?dl=0

 This Figure is not normal and usual.

 What is your opinion about this issue?

Best wishes,