[gmx-users] difficulties in creating octahedral boxes

[Ran Friedman]

Dear Astrid,

It seems as if the problem is in the presentation, not in GMX. trjconv
-ur compact may help.

Ran.

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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-- 
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
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