[gmx-users] octahedron box shape problem

thomas stockner thomas.stockner at uni-graz.at
Wed Oct 31 15:32:26 CET 2001


I am trying to generate an octahedron or dodecahedron box for a MD 
simulation, but unfortunately I  am not succesful. I get only rectangular 

I am using Gromacs version 3.0.5

applying a commands like:
-editconf -f struc.g96 -o box.g96 -d 1.4 -bt octahedron -label A 
-genbox -cp box.g96 -cs spc216.gro -o h2o.g96 -p struc.top 
and creating a pdb file for visualizing with rasmol
-pdb2gmx -f h2o.g96 -o rasmol.pdb
the box I get is always recangular, independenty which options of editconf I 
tryed (-bt; -angles; -box). 
I don't understand, why the output of editconf regarding the box statistic 
does not correspond to characteristics of the filled water box of the pdb 
file visualised with rasmol.

I cannot find the error I make. Could anyone help me to generate an 
octahedron box.




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Thomas Stockner
Institut of Chemistry
University Graz
Heichrichstrasse 28
8010 Graz

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