<br>I looked at g_rmsf -h but the problem is that it's not clear enough.<br>The help doesn't state how g_rmsf works & what does it calculate exactly.<br>Because the definition of an RMSF is the following: "the mean-square fluctuation is a measure of the deviation between the position of particle i and some reference position. Typically, this reference position will be the time-averaged position of the same particle i."<br>
So does g_rmsf calculate the average structure & then the RMSF according to this average structure?<br>Or does it calculate the RMSF after fitting to a reference structure that I would have specified with the option -s?<br>
<br>Thanks<br>Carla<br><br><div class="gmail_quote">On Tue, Feb 16, 2010 at 3:54 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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="im">On 17/02/10 01:12, Carla Jamous wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi everyone,<br>
please I need to calculate RMSF after fitting to the average structure<br>
of my MD simulation.<br>
Can anyone tell me how to do that? (especially, how to calculate the<br>
average structure)<br>
</blockquote>
<br></div>
g_rmsf. There's a section in the manual that gives a breakdown of the GROMACS tools by topic that can help guide you.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Another question that may sound stupid: does the "-s" have the same<br>
function with trjconv & g_rmsf? Can anyone clarify this option for me?<br>
</blockquote>
<br></div>
Use the -h flag to the tool to see a description of how things work.<br>
<br>
Mark<br><font color="#888888">
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