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On 18/12/2011 8:00 PM, Alex Jemulin wrote:
<blockquote
cite="mid:1324198836.80137.YahooMailNeo@web132406.mail.ird.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:times
new roman, new york, times, serif;font-size:12pt">
<div>Dear All</div>
<div> </div>
<div>I run a 1ns MD on a membrane protein and I get these values
for box coordinate's</div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;"><span style="font-family:
"Verdana","sans-serif"; font-size: 10pt;
mso-bidi-font-family: Calibri; mso-bidi-theme-font:
minor-latin; mso-ansi-language: EN-US;" lang="EN-US">Energy<span
style="mso-spacerun: yes;"> </span>Average<span
style="mso-spacerun: yes;"> </span>Err.Est.<span
style="mso-spacerun: yes;"> </span>RMSD<span
style="mso-spacerun: yes;">
</span>Tot-Drift<!--?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /--><o:p></o:p></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;"><span style="font-family:
"Verdana","sans-serif"; font-size: 10pt;
mso-bidi-font-family: Calibri; mso-bidi-theme-font:
minor-latin; mso-ansi-language: EN-US;" lang="EN-US">-------------------------------------------------------------------------------<o:p></o:p></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;"><span style="font-family:
"Verdana","sans-serif"; font-size: 10pt;
mso-bidi-font-family: Calibri; mso-bidi-theme-font:
minor-latin; mso-ansi-language: EN-US;" lang="EN-US">Box-X<span
style="mso-spacerun: yes;"> </span>13.867<span
style="mso-spacerun: yes;"> </span>0.071<span
style="mso-spacerun: yes;">
</span>0.167634<span style="mso-spacerun: yes;"> </span>0.48292<span
style="mso-spacerun: yes;"> </span>(nm)<o:p></o:p></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;"><span style="font-family:
"Verdana","sans-serif"; font-size: 10pt;
mso-bidi-font-family: Calibri; mso-bidi-theme-font:
minor-latin; mso-ansi-language: EN-US;" lang="EN-US">Box-Y<span
style="mso-spacerun: yes;"> </span>13.867<span
style="mso-spacerun: yes;"> </span>0.071<span
style="mso-spacerun: yes;">
</span>0.167634<span style="mso-spacerun: yes;"> </span>0.48292<span
style="mso-spacerun: yes;"> </span>(nm)<o:p></o:p></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;"><span style="font-family:
"Verdana","sans-serif"; font-size: 10pt;
mso-bidi-font-family: Calibri; mso-bidi-theme-font:
minor-latin; mso-ansi-language: EN-US;" lang="EN-US">Box-Z<span
style="mso-spacerun: yes;"> </span>9.15929<span
style="mso-spacerun: yes;"> </span>0.095<span
style="mso-spacerun: yes;">
</span>0.222463<span style="mso-spacerun: yes;"> </span>-0.642479<span
style="mso-spacerun: yes;"> </span>(nm)<o:p></o:p></span></div>
<div>
</div>
<div style="margin: 0cm 0cm 0pt;"><span style="font-family:
"Verdana","sans-serif"; font-size: 11pt;
mso-bidi-font-family: Calibri; mso-bidi-theme-font:
minor-latin; mso-ansi-language: EN-US;" lang="EN-US"><o:p><font
face="Times New Roman" size="3"> </font></o:p></span></div>
<div>
BoxX and BoxY fluctuate between <span style="line-height:
115%; font-family:
"Verdana","sans-serif"; font-size: 11pt;
mso-bidi-font-family: Calibri; mso-bidi-theme-font:
minor-latin; mso-ansi-language: IT; mso-fareast-font-family:
Calibri; mso-fareast-theme-font: minor-latin;
mso-fareast-language: EN-US; mso-bidi-language: AR-SA;">13,5
and
14,2 nm , BoxZ <font size="3"><font face="Times New Roman">fluctuate
between <span style="line-height: 115%; font-family:
"Verdana","sans-serif"; font-size:
11pt; mso-bidi-font-family: Calibri;
mso-bidi-theme-font: minor-latin; mso-ansi-language:
IT; mso-fareast-font-family: Calibri;
mso-fareast-theme-font: minor-latin;
mso-fareast-language: EN-US; mso-bidi-language:
AR-SA;">8,6 e 9,6
nm.</span></font></font></span></div>
<div><span style="line-height: 115%; font-family:
"Verdana","sans-serif"; font-size: 11pt;
mso-bidi-font-family: Calibri; mso-bidi-theme-font:
minor-latin; mso-ansi-language: IT; mso-fareast-font-family:
Calibri; mso-fareast-theme-font: minor-latin;
mso-fareast-language: EN-US; mso-bidi-language: AR-SA;"><font
size="3"><font face="Times New Roman"><span
style="line-height: 115%; font-family:
"Verdana","sans-serif"; font-size:
11pt; mso-bidi-font-family: Calibri;
mso-bidi-theme-font: minor-latin; mso-ansi-language:
IT; mso-fareast-font-family: Calibri;
mso-fareast-theme-font: minor-latin;
mso-fareast-language: EN-US; mso-bidi-language:
AR-SA;">These values seem not to reach a convergence.</span></font></font></span></div>
<div><span style="line-height: 115%; font-family:
"Verdana","sans-serif"; font-size: 11pt;
mso-bidi-font-family: Calibri; mso-bidi-theme-font:
minor-latin; mso-ansi-language: IT; mso-fareast-font-family:
Calibri; mso-fareast-theme-font: minor-latin;
mso-fareast-language: EN-US; mso-bidi-language: AR-SA;"><font
size="3"><font face="Times New Roman"><span
style="line-height: 115%; font-family:
"Verdana","sans-serif"; font-size:
11pt; mso-bidi-font-family: Calibri;
mso-bidi-theme-font: minor-latin; mso-ansi-language:
IT; mso-fareast-font-family: Calibri;
mso-fareast-theme-font: minor-latin;
mso-fareast-language: EN-US; mso-bidi-language:
AR-SA;">Which could be the cause? How can I fix it?</span></font></font></span></div>
</div>
</blockquote>
<br>
Does your experience of the membrane simulation literature suggest
that equilibration normally occurs over 1ns? In the absence of any
description of the starting point or procedure you used, nobody will
be able to say anything.<br>
<br>
Mark<br>
<br>
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