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<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Dear gromacs users,</span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>I am a beginner for gromacs. Now I try to simulate a
stretching behavior of a simple alpha-helix in aqueous solvent. In this system,
the helix consists of 123 atoms, and SOL molecule is 4281. I adopted afm mode
in *.ppa file. During the simulation, the helix structure is just stretched into
a ribbon structure. So the expected shift of potential energy of system is
about several hundreds kJmol-1, but in the obtained figure (potential energy
vs. time), the fluctuation is huge and even overwhelms the expected shift.</span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>I think this huge fluctuation can be due to the existence
of a lot of SOL molecules. Then the disturbance of system, e.g. thermal, can
cause a big accumulated fluctuation. </span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>About this problem, can I reduce it using some possible
ways? Or is it inevitable?</span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Thanks for any help and advice.</span></font></p>
<p><font size=2 face=宋体><span lang=EN-US style='font-size:10.0pt'>Best
regards,</span></font></p>
<p><font size=2 face=宋体><span lang=EN-US style='font-size:10.0pt'>Lixian,
Zhang</span></font></p>
<p><font size=2 face=宋体><span lang=EN-US style='font-size:10.0pt'>Max
Planck Institute for Metals Research<br>
Heisenbergstr. 3<br>
D-70569 </span></font><font size=2><span lang=EN-US style='font-size:10.0pt'>Stuttgart</span></font><font
size=2><span lang=EN-US style='font-size:10.0pt'><br>
</span></font><font size=2><span lang=EN-US style='font-size:10.0pt'>Germany</span></font><font
size=2><span lang=EN-US style='font-size:10.0pt'><br>
Tel: +49 (0) 711 689 3578<br>
Email:<a href="mailto:lixian.zhang@mf.mpg.de">lixian.zhang@mf.mpg.de</a> </span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span lang=EN-US> </span></font></p>
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