[gmx-users] difficulties in creating octahedral boxes

[Tsjerk Wassenaar]

Hi Astrid,

Besides all the useful advice regarding the visualization, note that
the rhombic dodecahedron is smaller than the truncated octahedron and
is more spherical, thus yields a more even distribution of water
around your solvent, rendering an effect due to the box type less
probable. In short, it's better to use a rhombic dodecahedron than a
truncated octahedron.

Cheers,

Tsjerk

On 12/11/06, Hanna, Joanne <J.F.Hanna at warwick.ac.uk> wrote:
>
>
>
> Hi
>
>  If you do:
>  editconf -f box.gro -o box.pdb
>  and view this in rasmol entering the command
>  set unitcell on
>  you should see the octahedral box.
>  To view the octahedral box with the water you need to use the '-ur compact'
> option in trjconv.
>  This should give you the octahedral representation.
>
>  Jo
>
>
>
>
>  -----Original Message-----
>  From: gmx-users-bounces at gromacs.org on behalf of Astrid Maaß
>  Sent: Mon 11/12/2006 10:53
>  To: gmx-users at gromacs.org
>  Subject: [gmx-users] difficulties in creating octahedral boxes
>
>  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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623