[gmx-users] pbc problem

[Atila Petrosian]

Dear Gromacs users

I did simulation of a system containing protein and cnt using gromacs 4.5.6.

When I see trajectory by VMD, in some frames, protein atoms exit one side
of box
and enter opposite side of box (pbc problem). I know I should use -pbc
option of
trjconv tool. But I do not know exactly which of none, mol, res, atom,
nojump,
cluster or whole is appropriate for me. The below link shows one frame of
trajectory:

https://www.dropbox.com/s/vur8fh1apvp79lm/pbc%20problem.bmp

Any help will highly appreciated