[gmx-users] difficulties in creating octahedral boxes

[David van der Spoel]

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.
________________________________________________________________________
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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