[gmx-users] PBC problem in bilayer system

[shahab shariati]

Dear Justin

Thanks for your answer.

You said " The raw output of g_traj in this case is not very useful "

I want to know position and location of drug molecules relative to the DPPC
bilayer during simulation time.

In your opinion, how should I use this tool (g_traj)?

Is g_dist appropriate for obtaining distance between center of mass of the
drug molecules and DPPC lipid bilayer as a function of simulation time?


Best wishes.