[gmx-users] difficulties in creating octahedral boxes

Hanna, Joanne J.F.Hanna at warwick.ac.uk
Mon Dec 11 17:02:09 CET 2006


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.


-----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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