[gmx-users] PBC problem in bilayer system

shahab shariati shahab.shariati at gmail.com
Tue Sep 9 16:11:11 CEST 2014

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.

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