[gmx-users] PBC problem in bilayer system

[shahab shariati]

Dear Justin

Thanks for your reply.

I inserted 4 drug molecules in close vicinity to the membrane surface
in water phase, in one side of bilayer (for example, top). In the
different frames of trajectory, some of drug molecules (one or two
drug molecules) are seen in other side of bilayer (bottom).  I really
do not know what thing has to be translated. Should I shift all
components of my system (DPPC, drug, and water molecules) along z or
only drug molecules?



The dimensions of my system in final gro file are as follows:

 6.46063   6.57889   8.30034



Based on your reply (The exact magnitude depends on the dimensions of the
system), should I use following command:



trjconv –trans 6.46063   6.57889   8.30034