Hello again,<br><br>I tried comparing RDF plots generated by sampling from 4 to 5 ns run and a longer run from 4 to 30 ns to see whether the small jumps on the plot are due to insufficient sampling. Attached is the new plot showing that two RDF curves are almost identical. I only wanted to let you know and please comment on the attached plot if you have any ideas. Thank you. :)<br>
<br>Moeed<br><br><div class="gmail_quote">On Sat, Sep 10, 2011 at 10:00 AM, Moeed <span dir="ltr"><<a href="mailto:lecielll@googlemail.com" target="_blank">lecielll@googlemail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thank you for your input. I am going to run for another 15 ns to see if the little jumps vanish.<br><br>Best,<div><div></div><div><br><br><div class="gmail_quote">On Fri, Sep 9, 2011 at 9:16 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
<br>
lina wrote:<div><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
On Sat, Sep 10, 2011 at 3:35 AM, Moeed <<a href="mailto:lecielll@googlemail.com" target="_blank">lecielll@googlemail.com</a> <mailto:<a href="mailto:lecielll@googlemail.com" target="_blank">lecielll@googlemail.<u></u>com</a>>> wrote:<br>
<br>
Dear users,<br>
<br>
I have created radial distribution function plot for Carbon atoms in<br>
a system containing polymer chains. I see some little jumps between<br>
first and second peak.<br>
I need your help to comment on how this behavior can be justified<br>
(or if the plot is wrong).<br>
<br>
g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx <br>
Thank you in advance.<br>
<br>
<br>
I think your figure is fine.<br>
</blockquote>
<br>
<br></div>
I think, based on information given in subsequent messages, that there is insufficient data collection to assess whether this RDF plot is as meaningful as it could be. There is nothing glaringly wrong, but the roughness is due to insufficient sampling.<div>
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
You just need how to proper interpret your figures, truly understand what the "radial distribution" means.<br>
<br>
</blockquote>
<br></div>
I think it inappropriate to suggest that the OP does not understand the concept behind the figure; some guidance, perhaps is necessary, but nothing more.<div><br>
<br>
-Justin<br>
<br>
-- <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>
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