[gmx-users] pbc nojump with replica exchange behaves differently than with regular MD

[Ramon Crehuet]

Dear all, 
I have run a temperature replica exchange and I would like to analyze the resulting trajectory for a given temperature (i.e. not following a replica across temperatures using demux.pl). 
The simulations consist of a single protein chain. I can easily generate have a whole molecule, named `whole.pdb`. 
When I was running regular MD, the following worked fine to generate whole structures that diffused out of the box: 

gmx trjconv -f md.xtc -s whole.pdb -pbc nojump -o whole.xtc 

But repeating that for one of the md.xtc of the replica exchange does not work. Each atom diffuses or of the box (i.e. without jumps) but to different directions, resulting in an apparently exploding molecule. 
Should there be a different treatment of RE simulations? If so, what should I do? (I have tried the -pbc nojump step followed or preceded by -pbc whole without success). 
Thanks for your attention. 
Best, 
Ramon