[gmx-users] PBC problem in bilayer system

[shahab shariati]

Dear gromacs users

I did MD simulation of my system containing DPPC lipids + water molecule
and 4 drug molecules.

I saw trajectory file using VMD.

Unfortunately, drug molecules jump across the box.

How to resolve this PBC problem?

which of -pbc options (none, mol, res, atom, nojump, cluster or whole) in
trjconv tool is appropriate for my case?


Any help will highly appreciated.