[gmx-users] Dump with trjconv - periodic coordinates

Malin Bergenstråhle malbe at kth.se
Wed Jan 4 17:26:39 CET 2006


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,


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