[gmx-users] difficulties in creating octahedral boxes

David van der Spoel spoel at xray.bmc.uu.se
Mon Dec 11 12:00:38 CET 2006

Astrid Maaß wrote:
> 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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please read the manual, in particular chapter three, which explains 
periodic boundary conditions and the different boxes.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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