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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 style='font-size:10.0pt;
font-family:Arial'>I have been a bit confused by the g_rmsf output. In the
manual, it says that “g_rmsf computes the root mean square fluctuation
(RMSF, i.e. standard deviation) of atomic positions after first fitting to a
reference frame.” But what *<b><span style='font-weight:bold'>is</span></b>*
the reference frame?<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 style='font-size:10.0pt;
font-family:Arial'>I assume that this output is what goes to the file specified
by –o (rmsf.xvg, by default).<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 style='font-size:10.0pt;
font-family:Arial'>The –od option (which goes to rmsdev.xvg by default) is
the rms deviation “with respect to the reference structure”. What
reference structure? Is that the same as the “reference frame”
mentioned above? I notice that the numbers in rmsf.svg and rmsdev.xvg are
always different, so I assume not. <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 style='font-size:10.0pt;
font-family:Arial'>Can anyone explain the difference between what goes into the
–o file, and what goes into the –od file?<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 style='font-size:10.0pt;
font-family:Arial'>Also, if I start at a specific frame (say, -b 1000, to start
1ns into the trajectory), is the conformation nearest t=1ns the reference
frame/structure?<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 style='font-size:10.0pt;
font-family:Arial'>Many thanks,<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 style='font-size:10.0pt;
font-family:Arial'> Keith<o:p></o:p></span></font></p>
<p style='margin-bottom:0in;margin-bottom:.0001pt'><font size=2
face="Times New Roman"><span style='font-size:10.0pt'>============================<br>
</span></font><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'>Keith D. Ball, PhD<br>
Staff Scientist<br>
Catalyst Biosciences<br>
<st1:address tabIndex="0"
style="BACKGROUND-POSITION: left bottom; BACKGROUND-IMAGE: url(res://ietag.dll/#34/#1001); BACKGROUND-REPEAT: repeat-x"
w:st="on"><st1:Street w:st="on">290 Utah Ave</st1:Street><br>
<st1:place w:st="on"><st1:City w:st="on">S. San Francisco</st1:City>, <st1:State
w:st="on">CA</st1:State> <st1:PostalCode w:st="on">94080</st1:PostalCode></st1:place></st1:address></span></font><font
size=2><span style='font-size:10.0pt'><br>
<br>
</span></font><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'>650-266-8661 (phone)<br>
650-871-2475 (fax)<br>
<a href="mailto:kball@catbio.com">kball@catbio.com</a></span></font><font
face=Verdana><span style='font-family:Verdana'><o:p></o:p></span></font></p>
<p style='margin:0in;margin-bottom:.0001pt'><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana'><a href="http://www.catbio.com">http://www.catbio.com</a></span></font><font
size=2><span style='font-size:10.0pt'><br>
============================<o:p></o:p></span></font></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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