[gmx-users] from beginners: how to center?

Mr.wolf_79 mr.wolf_79 at email.it
Mon Mar 1 11:57:00 CET 2004

Dear users, 
we are pretty new to gromacs, so please be patient...
The question is about the box of solvent: how to center the system in this
box? Visualizing the results of the tutor exercises (water molecules for
instance) with the ngmx command, the box of solvent is only partially inside
the yellow lines defining the volume of the box. This happens also with
other proteins we used: we tried several times genbox with options -box and
-c (thus we expected to see the system centered) but the molecule appears
above the yellow box...
Playing around with coordinate values of the center to pass to genbox, we
ended up succesfully in centering the molecule, but then the solvent
doesn\'t follow: spc molecules and the box are staggered... 

Davide Ruffoni & Mario Orsi
Politecnico di Milano

\"At least I\'m housebroken\" (The Big Lebowsky)

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