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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hi,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>I simulate a molecule in a dodecahedron.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>I used at the step with the editconf:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>editconf -f name.gro -o name.dod.pdb -bt dodecahedron
-d 2.0<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>After my simulation I looked at the first frame and
saw, that at two direction the molecule is actually 2 nm away of my edge, but
the at the third edge the molecule is not in the middle, but near the edge.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>I looked also at the other pdb-files with the water
before the simulation, and there the location of the molecule is the same, in
my opinion not in the middle of the body.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>Is this a bug? Or have I done anything wrong?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>Thanks a lot for your helps!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>Greets, Birgit<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>---</span></font><span lang=EN-GB><o:p></o:p></span></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span lang=EN-GB
style='font-size:10.0pt'>DI Birgit Hischenhuber</span></font><span lang=EN-GB><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span lang=EN-GB
style='font-size:10.0pt'>Unit for Medical Statistics and Informatics </span></font><span
lang=EN-GB><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span lang=EN-GB
style='font-size:10.0pt'>Section for Biomedical Computersimulation and
Bioinformatics</span></font><span lang=EN-GB><o:p></o:p></span></p>
<p class=MsoNormal><st1:PlaceName w:st="on"><font size=2 face="Times New Roman"><span
lang=EN-GB style='font-size:10.0pt'>Medical</span></font></st1:PlaceName><font
size=2><span lang=EN-GB style='font-size:10.0pt'> <st1:PlaceType w:st="on">University</st1:PlaceType>
of <st1:City w:st="on"><st1:place w:st="on">Vienna</st1:place></st1:City></span></font><span
lang=EN-GB><o:p></o:p></span></p>
<p class=MsoNormal><st1:place w:st="on"><st1:PlaceName w:st="on"><font size=2
face="Times New Roman"><span lang=EN-GB style='font-size:10.0pt'>General</span></font></st1:PlaceName><font
size=2><span lang=EN-GB style='font-size:10.0pt'> <st1:PlaceType w:st="on">Hospital</st1:PlaceType></span></font></st1:place><span
lang=EN-GB><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
10.0pt'>Spitalgasse 23, BT88</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
10.0pt'>A-1090 Vienna</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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