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<P><FONT SIZE=2>Hi<BR>
<BR>
If you do:<BR>
editconf -f box.gro -o box.pdb<BR>
and view this in rasmol entering the command<BR>
set unitcell on<BR>
you should see the octahedral box.<BR>
To view the octahedral box with the water you need to use the '-ur compact' option in trjconv.<BR>
This should give you the octahedral representation.<BR>
<BR>
Jo<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org on behalf of Astrid Maaß<BR>
Sent: Mon 11/12/2006 10:53<BR>
To: gmx-users@gromacs.org<BR>
Subject: [gmx-users] difficulties in creating octahedral boxes<BR>
<BR>
Dear all,<BR>
<BR>
I am new to gromacs and exercising, thus currently I am trying to follow<BR>
the "Gromacs tutorial for Drug-Enzyme complex" of J. Kerrigan (many<BR>
thanks) for my example molecule (alanine). I have used the sequence of<BR>
commands below:<BR>
<BR>
pdb2gmx -f example.pdb -p ex.top -o ex_in.gro<BR>
editconf -f ex_in.gro -d 1.0 -bt octahedron -c -o ex_in_box.gro<BR>
genbox -cp ex_in_box.gro -cs -o ex_sol.gro -p ex.top<BR>
genbox -cp ex_in_box.gro -cs -o ex_sol.pdb -p ex.top<BR>
<BR>
When viewing my system ex_sol.pdb with rasmol I notice that my alanine<BR>
molecule is placed near to one face (inspite of -c) of a rectangular<BR>
(inspite of -bt octahedron) box. editconf gives no warning and the final<BR>
line in ex_in_box.gro seems to describe a non cubic box:<BR>
2.43930 2.29979 1.99168 0.00000 0.00000 0.81310 0.00000 <BR>
-0.81310 1.14989<BR>
When filling the box with water molecules by use of genbox again no<BR>
significant warning is given and the final line remains unaltered in<BR>
ex_sol.gro. So why do I see my alanine in a cube of water molecules?<BR>
<BR>
I would appreciate any explanation or instruction how to create a<BR>
non-cubic system very much.<BR>
Thank you in advance!<BR>
<BR>
Kind regards,<BR>
<BR>
Astrid Maaß<BR>
<BR>
<BR>
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