[gmx-users] Dump with trjconv - periodic coordinates

[Malin Bergenstråhle]

Hi,

When I make a coordinate dump from a trajectory with
trjconv -dump to a .gro - file
I get a coordinate file where the coordinates are sometimes out of the 
periodic box.
Is this normal, or could there be a problem?

I use pbc=full and try to simulate an "infinite" polymer, covalently 
bonded over the periodic boundary.
I have (still) problems with atoms at the periodic boundaries causing 
simulation crash due to Lincs complaining about bond rotations.



Best regards,

Malin