[gmx-users] difficulties in creating octahedral boxes
astrid.maass at scai.fhg.de
Mon Dec 11 11:53:31 CET 2006
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
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
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!
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