[gmx-users] pbc problem

Atila Petrosian atila.petrosian at gmail.com
Sun Feb 2 13:15:43 CET 2014

Dear Justin and Tsjerk

you said " Some tools handle PBC properly, some don't ".

I want to know exactly which tools of gromacs handle PBC properly.

Can I find these tools in manual?

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. I want to do analysis of trajectory. I do
not know
exactly this state is pbc problem or not.

Any help will highly appreciated

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