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

Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl
Mon Mar 1 12:13:01 CET 2004


You would do better using editconf for centering the molecule in the 
box. In gromacs versions < 3.2 you can do that with the -c option, in 
3.2 there's a bug and you will have to do it 'by hand' using the option 
-center. The geometrical center for the (triclinic) box can be 
calculated from the three or nine numbers you find at the end of your 
.gro file, numbered here box1 - box9:

editconf -f in.gro -o out.gro -center 0.5*(box1 + box6 + box8) 0.5*(box2 
+ box4 + box9) 0.5*(box3 + box5 + box7)



Mr.wolf_79 wrote:

> 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...
> Thanks!
> Davide Ruffoni & Mario Orsi
> Politecnico di Milano
> "At least I'm housebroken" (The Big Lebowsky)
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