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

GtrAngus maps99 at online.de
Mon Mar 31 23:39:53 CEST 2014

Hi :)

I am having a little problem with my cubic box full of water. I am trying to
calculate the polarization density so I divide the box into different layers
in Z-direction and do my calculation for every layer. The box goes from 0 nm
to 4 nm in every direction. Now I realized that some of my atoms were not
taken into consideration because they have negative Z-coordinates! How do I
have to change the PBC to avoid this problem? :)

Does a negative value of e.g. -0.1 mean the atom has the position 3.9 in
reality? If that's true then I can fix this myself with my C-Code.

Thanks for any help!

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