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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 peptide in a water box with some ions to
get a neutral solution. I want to visualize the peptide in the water box.<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 want that the peptide is in the center of the box,
but also have a look at the water.<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'>Therefore I tried two things:<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'>trjconv –f a.trr –o b.xtc –s c.tpr –skip
10 –pbc mol –<st1:City w:st="on"><st1:place w:st="on">ur</st1:place></st1:City>
compact –center –fit progressive<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'>Visualizing it with VMD I see the peptide centering
in the middle of the box, but the water get during the time holes.<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'>So I checked the mailing list and find some inputs
and tried it with two steps:<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'>trjconv –f a.trr –o b.xtc –s c.tpr –pbc
mol –<st1:City w:st="on"><st1:place w:st="on">ur</st1:place></st1:City> compact<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'>trjconv –f b.xtc –o d.xtc –s c.tpr –skip
10 –center –fit progressive<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'>at this try I get a peptide in the center of the box
and during the time the pepide moves to the edge of the box and I consider that
the box rotate around the peptide.<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 there a possibility that my peptide stays in the
center of the box and the water doesn’t get any holes?<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'>---</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><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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