[gmx-users] pbc problem

Atila Petrosian atila.petrosian at gmail.com
Wed Jan 29 11:09:08 CET 2014

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,
cluster or whole is appropriate for me. The below link shows one frame of


Any help will highly appreciated

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