<div>Not R_x, R_y, and R_z.</div>
<div> </div>
<div>What I want to obtain are the three three principal moments of the ellipsoidal macromolecule.</div>
<div> </div>
<div>They are different quantities.</div>
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<div class="gmail_quote">2011/5/10 Erik Marklund <span dir="ltr"><<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Mark Abraham skrev 2011-05-10 12.31:
<div class="im"><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">On 10/05/2011 8:23 PM, lammps lammps wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Hi,<br>I want to study the shape change of a macromolecule which seems like a ellipsoid. So, I need obtain the three principal moments of the molecules.<br>
Is the command of g_gyrate helpful for me? The sum of the three principal moments should be equal to the <Rg^2>. However, I used the command g_gyrate -f traj.gro -s nvt.tpr -n anly.ndx -o shape.xvg -p obtain the Rg and other three qualities.<br>
It seems that the sum of the last three qualities is not equal to the Rg^2. Is there something wrong?<br></blockquote><br>Why should that sum equal Rg^2?<br><br>Mark<br></blockquote></div>Shouldn't it be half of that sum?<br>
<br> Rg^2 = 1/N Sum([r_k - <r>]^2),<br><br>where r are vectors and masses are set to unity for conveniance. If decomposed in orthonormal axes x, y, and z, it yealds<br><br> Rg^2 = 1/N Sum([x_k-<x>]^2 + [y_k-<y>]^2 + [z_k-<z>]^2).<br>
<br>The radius of gyration around e.g. the x-axis is<br><br> Rg_x^2 = !/N Sum([y_k-<y>]^2 + [z_k-<z_k>]^2).<br><br>Hence Rg^2 = (Rg_x^2+Rg_y^2+Rg_z^2) / 2.<br><br>That matches the numbers I get from my tests.<br>
<font color="#888888"><br>-- <br>-----------------------------------------------<br>Erik Marklund, PhD student<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: +46 18 471 4537 fax: +46 18 511 755<br><a href="mailto:erikm@xray.bmc.uu.se" target="_blank">erikm@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a></font>
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