[gmx-users] PBC problem in bilayer system

Michael Carter Michael.Carter at icr.ac.uk
Tue Sep 9 16:13:58 CEST 2014


Try -pbc nojump


On 09/09/2014 15:11, "shahab shariati" <shahab.shariati at gmail.com> wrote:

>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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