[gmx-users] PBC problem

[Andrea Carotti]

Hi gmx-ers,
    I'm trying to visualize with vmd my trajectory (only the protein,
without water). I think I'm having problem with the pbc option of trjconv.
During the simulation (in vmd) a chain of my protein jumping. It's for sure
that this appens when that portion of protein goes out from the box
(octhaedron type).
I've tried -pbc nojump -center (using the protein group) and -pbc
whole -center -fit progressive but without success.
Please someone could  suggest me something to check or to try
Thanks
Andrea