[gmx-users] difficulties in creating octahedral boxes

Astrid Maaß astrid.maass at scai.fhg.de
Mon Dec 11 11:53:31 CET 2006

Dear all,

I am new to gromacs and exercising, thus currently I am trying to follow 
the "Gromacs tutorial for Drug-Enzyme complex" of J. Kerrigan (many 
thanks) for my example molecule (alanine).  I have used the sequence of 
commands below:

pdb2gmx -f example.pdb -p ex.top -o ex_in.gro
editconf -f ex_in.gro -d 1.0 -bt octahedron -c -o ex_in_box.gro
genbox -cp ex_in_box.gro -cs -o ex_sol.gro -p ex.top
genbox -cp ex_in_box.gro -cs -o ex_sol.pdb -p ex.top

When viewing my system ex_sol.pdb with rasmol I notice that my alanine 
molecule is placed near to one face (inspite of -c) of a rectangular 
(inspite of -bt octahedron) box. editconf gives no warning and the final 
line in ex_in_box.gro seems to describe a non cubic box:
2.43930   2.29979   1.99168   0.00000   0.00000   0.81310   0.00000  
-0.81310   1.14989
When filling the box with water molecules by use of genbox again no 
significant warning is given and the final line remains unaltered in 
ex_sol.gro. So why do I see my alanine in a cube of water molecules?

I would appreciate any explanation or instruction how to create a 
non-cubic system very much.
Thank you in advance!

Kind regards,

 Astrid Maaß

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