Dear Justin,<br>Thanks for your reply.<br>Tsjerk: <a href="http://lists.gromacs.org/pipermail/gmx-users/2009-October/045884.html">http://lists.gromacs.org/pipermail/gmx-users/2009-October/045884.html</a><br><br><blockquote>
<blockquote style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;" class="gmail_quote">There are two things to distinguish:<br><br>1. The reference structure used to remove translational and rotational<br>
degrees of freedom<br>2. The reference against which the deviations (on a per atom base) are<br>calculated that are then squared, averaged and taken the root of (root<br>mean square fluctuation).<br><br>These two need not be the same. It is common, and most sensible, to<br>
calculate the deviations against the average structure, after fitting<br>all structures in the trajectory against a certain reference<br>structure. With option -od the deviations against the reference used<br>for fitting are calculated rather than against the average. You do<br>
need a reference for fitting, since otherwise you include overall<br>rotation and translation in the calculation of the RMSF, which you<br>usually wouldn't want.<br></blockquote></blockquote><br>1.) For RMSD, You said (i.e. the one present in the .tpr file). which one? <span id="result_box" class="short_text" lang="en"><span class="hps">How do Gromacs select</span> <span class="hps">the reference</span> <span class="hps">structure</span></span>?<br>
<br>2.) Tsjerk: RMSF calculate the deviations against the average structure, after fitting all structures in the trajectory against a certain reference structure.<br><br>the reference structure is taken as average over the trajectory. That is, it is the average structure (please look at example). isn't it?<br>
<u>For example:</u><br>coordinates of N atom:<br>x y z<br>2 4 6 <br>8 7 1<br>8 1 2<br>the average structure of N atom:[(x1+x2+x3)/3, (y1+y2+y3)/3, (z1+z2+z3)/3]. isnt it?<br>x y z<br>6 4 3<br><br>3.) This "The reference structure used to remove translational and rotational degrees of freedom" is RMSD???<br>
<br><br><div class="gmail_quote">2011/9/21 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><div class="h5"><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear users,<br>
<br>
g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res<br>
<br>
With the option -od the root mean square deviation with respect to the reference structure is calculated.<br>
Then,<br>
RMSDEV is the RMSD per residue (the root mean square deviation with respect to the reference structure is calculated).<br>
<br>
and<br>
RMSF is the RMSD per residue (the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame). That is, it is the measurement averaged over all atoms in each residue.<br>
<br>
Now what difference?<br>
<br>
</blockquote>
<br></div></div>
The RMSD is measured relative to the reference structure (i.e. the one present in the .tpr file). RMSF is measured with respect to average coordinates.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I am confused.<br>
<br>
-- <br>
Ahmet YILDIRIM<br>
<br>
</blockquote>
<br></div>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>