[gmx-users] Water out of box? Negative Z-Coordinates

[GtrAngus]

Justin Lemkul wrote
> That observation conflicts with the very definition of what -pbc atom
> does.  How 
> large is the box?  Do you have correct vectors in the trajectory?  I still
> don't 
> know why mdrun produced negative coordinates in the first place - the run
> was 
> done with mdrun, correct?

conf.gro and confout.gro say the box is 4.00000  4.00000  4.00000

I just saw: the atoms in conf.gro are already out of the box and some have
coordinates <0 or >4 ?!

The job was done via a so called job_script for a cluster. The job_script
includs the command "srun_ps mdrun_mpi". So I asume the answer is: yes.

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