<div dir="ltr">Dear David,<br><br>I tried to calculate the S2 order parameters using g_rotacf. I removed the rotational and translational degrees of freedom from my trajectory using:<br><br>trjconv -f -s -o -fit rot_trans<br>
<br>Then used this new trajectory to calculate the correlation functions using g_rotacf:<br><br>g_rotacf -f -s -o -P 2 -d -n -noaver<br><br>The index file contains N-H bond vectors and the simulation I ran is for 50 ns.<br>
<br>The decay of the correlation function is smooth and after a while it is pleatue (parallel to time axis). I averaged the second half of the correlation function values for each vector. I think these corresponds to the S2 order paramters. But a few of them turned out to be negative which are not supposed to be I believe. Is there any reason for this or am I making any mistake in the process.<br>
<br>Thanks in advance,<br>Ram.<br><br><div class="gmail_quote">On Thu, Sep 11, 2008 at 2:30 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d">rams rams wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear users,<br>
<br>
The S2 order parameters obtained by using g_chi, are they corresponds to the Lipari_Szabo NMR order parameters for characterizing the internal motions?<br>
</blockquote></div>
No, they are described here:<br>
<br>
D. van der Spoel and H.J.C. Berendsen: Molecular dynamics simulations of Leu-Enkephalin in water and DMSO Biophys. J. 72 pp. 2032-2041 (1997)<div class="Ih2E3d"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Also it is mentioned in the manual that the obtained S2 parameter corresponds to a dihedral and the generated plot is residue vs S2. Does it mean that the S2 parameters are averaged on each residue ??<br>
</blockquote></div>
No, you have one values for each dihedral.<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Thanks in advance.<br>
Ram.<br>
<br>
<br>
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David van der Spoel, Ph.D., Professor of Biology<br>
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