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<title>RE: [gmx-users] difficulties in creating octahedral boxes</title>
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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Guys, <o:p></o:p></span></font></p>
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use genion with –np 2. However it seemed to recognize that there were
already two in the file and added none. So instead I used the parameter –np
4. This seemed to add two, for a total of four, which I wanted. However
sometimes it seems to add two too many! Am I understanding the proper use of
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Hanna, Joanne<br>
<b><span style='font-weight:bold'>Sent:</span></b> Monday, December 11, 2006
11:02 AM<br>
<b><span style='font-weight:bold'>To:</span></b> Discussion list for GROMACS
users<br>
<b><span style='font-weight:bold'>Subject:</span></b> RE: [gmx-users]
difficulties in creating octahedral boxes</span></font><o:p></o:p></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p style='margin-bottom:12.0pt'><font size=2 face="Times New Roman"><span
style='font-size:10.0pt'>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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