[gmx-users] View Trajectory - Water Expansion

Natalie Stephenson natalie.stephenson at manchester.ac.uk
Thu Feb 11 13:13:30 CET 2016

Hi all,

I'm experiencing a problem with my trajectory waters. Really early on in the simulation the waters begin expanding out of the box. There are no system errors that I am aware of and the simulation runs fine.

Is this something that can be fixed with trjconv? Or is it something more worrying with regards to the simulation run? I'm currently using trjconv with -pbc nojump, resulting in the protein looking fine, but the waters are another matter.

I've tried searching for this issue but couldn't find other mention of it.

Thanks for any help that you can offer.


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