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

[GtrAngus]

Justin Lemkul wrote
> Well, what did you do to observe negative coordinates?  In principle, all
> unit 
> cells in Gromacs have an origin at (0,0,0) and the way mdrun works you
> should 
> only get positive coordinates, IIRC.  So the emergence of negative
> coordinates 
> is a bit odd, but there's nothing wrong with it.


I faced the problem while I made a sum over all dipolmoments. Every time I
calculated it, the counter goes ++. The number varies for every loop so I
made a if-loop with if(pos[i][ZZ] < 0) and a new counter counts the atoms
with a negative Z-coordinate.



Justin Lemkul wrote
> Yes, assuming your box dimensions are invariant (i.e. NVT/NVE), but
> trjconv 
> should handle this so you don't have to reinvent the wheel.

Yes, it is NVT. I looks like you are familiar to trjconv ! :) I looked it up
in the manual. Is this syntax correct for my problem?

> trjconv -f traj.trr -pbc atom

Or which one would you prefer?

Thx for your fast answer Justin Lemkul!


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