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<p style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Hi!</font></p>
<p style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">I have a 7ns MD run of a protein and the RMSD of the protein had stabilized after 3ns. </font></p>
<p style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">I am about to performed essential dynamics (ED) analysis (using the commands g_covar and g_anaeig) on the trajectory and I have a few questions/clarifications.</font></p>
<p style="MARGIN: 0in 0in 0pt"><font size="3"><font face="Times New Roman">1) Should ED analysis be performed only on the segment of trajectory wherein the protein's RMSD has equilibrated,</font></font><font size="3"><font face="Times New Roman"> am I right? <span> </span>Because I have the notion that harmonic analysis of a trajectory can only be performed when the protein is undergoing fluctuations about a minimum. In other words once rmsd stabilizes, then one can perform a harmonic analysis.</font></font></p>
<p style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">2) Which would be a better marker to see if the protein has equilibrated to the simulation environment the RMSD of the protein or the projection of motion along Eigen vectors?</font></p>
<p style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">3) When I plot the root mean square fluctuation (r.m.s.f.) of the amino acids am I plotting the motions (of c-alphas) orthogonal to the principal component, Eigen vector 1? and w</font><font face="Times New Roman" size="3">ould I wrong in saying that these regions of the protein which have large fluctuations, (say greater than 2 angstroms), do experience anharmonic fluctuation? </font></p>
<p style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">If so how can I pick up anharmonic fluctuations?</font></p>
<p style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">Thank you</font></p>
<p style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3">JJ</font></p>
<p style="MARGIN: 0in 0in 0pt"><br clear="all"><font face="Times New Roman" size="3"> </font></p>
<p style="MARGIN: 0in 0in 0pt"><font face="Times New Roman" size="3"> </font></p></div>
<div></div><br>-- <br>Jayasundar Jayant James<br><br><a href="http://www.chick.com/reading/tracts/0096/0096_01.asp" target="_blank">www.chick.com/reading/tracts/0096/0096_01.asp</a>) <br><br>