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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'>I think it just says that samping of your
trajectory is not long enough. Each trajectory just sits in its own local
minimum.</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
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<p><font size=2 color=navy face="Times New Roman"><span style='font-size:10.0pt;
color:navy'>Regards<br>
Yuguang<br>
<br>
Dr. Yuguang Mu<br>
Division of Computational and Structrual Biology<br>
School of Biological Sciences<br>
Nanyang Technological University<br>
Singapore 637820<br>
Tel: 0065-63162885<br>
Mail: ygmu@ntu.edu.sg</span></font></p>
</div>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma'>-----Original Message-----<br>
<b><span style='font-weight:bold'>From:</span></b> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <b><span style='font-weight:bold'>On
Behalf Of </span></b>vincenzo venditti<br>
<b><span style='font-weight:bold'>Sent:</span></b> 2004</span></font><font
size=2 face=SimSun><span lang=ZH-CN style='font-size:10.0pt;font-family:SimSun'>Äê</span></font><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>11</span></font><font
size=2 face=SimSun><span lang=ZH-CN style='font-size:10.0pt;font-family:SimSun'>ÔÂ</span></font><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>25</span></font><font
size=2 face=SimSun><span lang=ZH-CN style='font-size:10.0pt;font-family:SimSun'>ÈÕ</span></font><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> 22:35<br>
<b><span style='font-weight:bold'>To:</span></b> gmx-users@gromacs.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [gmx-users] combined ED</span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> </span></font></p>
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<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Dear list,</span></font></p>
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<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>I've performed two MD on the same pdb file and with
the same mdp files,</span></font></p>
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<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>but when I perform the ED analysis on the concateneted
trajectory I find difference along the first eigenvector for the two
separate trajectories:</span></font></p>
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<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> </span></font></p>
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<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>-trajectory
1 -trajectory
2</span></font></p>
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<div>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> averages projection (1st eigenvec)=0.908
nm averages projection (1st eigenvec)=- 0.906 nm</span></font></p>
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<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> rmsf (1st eigenvec) =
0.031 nm
rmsf (1st eigenvec) = 0.017 nm</span></font></p>
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<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> </span></font></p>
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<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>I know that two MD simulations on the same
sistem difficultly are the same, but what do you think about the extent of the
differences?</span></font></p>
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<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> </span></font></p>
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<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Thanks in advance,</span></font></p>
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<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Vincenzo</span></font></p>
</div>
</div>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><br clear=all>
</span></font></p>
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size=3 face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=3 width="100%" align=center>
</span></font></div>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Ricerche online pi¡§´ semplici e veloci con <a
href="http://g.msn.com/8HMBITIT/2737??PS=47575" target="_top">MSN Toolbar</a> !</span></font></p>
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