[gmx-users] Location of a molecule in a dodecahedron

Birgit Hischenhuber birgit.hischenhuber at meduniwien.ac.at
Thu Jul 8 16:25:56 CEST 2010



I simulate a molecule in a dodecahedron.

I used at the step with the editconf:


editconf -f name.gro -o name.dod.pdb -bt dodecahedron -d 2.0


After my simulation I looked at the first frame and saw, that at two
direction the molecule is actually 2 nm away of my edge, but the at the
third edge the molecule is not in the middle, but near the edge.

I looked also at the other pdb-files with the water before the simulation,
and there the location of the molecule is the same, in my opinion not in the
middle of the body.


Is this a bug? Or have I done anything wrong?


Thanks a lot for your helps!


Greets, Birgit




DI Birgit Hischenhuber

Unit for Medical Statistics and Informatics 

Section for Biomedical Computersimulation and Bioinformatics

Medical University of Vienna

General Hospital

Spitalgasse 23, BT88

A-1090 Vienna


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