Thank you Dr Warren for your comment. I actually still need your help with your hint. I am not able to realize how to measure the distances..do I have to look at the plot and find the distance shown by the Peaks and then look at the same distance in VMD ? But which frames do I have to upload?<br>
<br>Please guide me a little more.<br><br>Thank you,<br><br><div class="gmail_quote">On Thu, Sep 15, 2011 at 6:26 PM, Dallas Warren <span dir="ltr"><<a href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.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;">
<div link="blue" vlink="purple" lang="EN-US">
<div>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Load up some frames into VMD and start measuring the distances shown by the peaks in your RDF, link them with what you actually see in there (using something
like a transparent representation of the carbon atom(s) using VDW then set the sphere scale so that it matches the correct radius, may be an easier way to do this, but this would make it easy to see). Appears it may be something real, so just check the coordinate
file and see where they are actually coming from.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Catch ya,<br>
<br>
Dr. Dallas Warren<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Medicinal Chemistry and Drug Action<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Monash Institute of Pharmaceutical Sciences</span><span style="font-size: 10pt; color: rgb(31, 73, 125);">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);"><a href="tel:%2B61%203%209903%209304" value="+61399039304" target="_blank">+61 3 9903 9304</a><br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size: 11pt; color: rgb(31, 73, 125);">
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"><u></u> <u></u></span></p>
<div style="border-width: medium medium medium 1.5pt; border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; padding: 0cm 0cm 0cm 4pt;">
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<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;"> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>]
<b>On Behalf Of </b>Moeed<br>
<b>Sent:</b> Friday, 16 September 2011 12:55 AM<br>
<b>To:</b> <a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>; Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] radial distribution function<u></u><u></u></span></p>
</div>
</div><div class="im">
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal" style="margin-bottom: 12pt;">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<u></u><u></u></p>
</div><div><div></div><div class="h5"><div>
<p class="MsoNormal">On Sat, Sep 10, 2011 at 10:00 AM, Moeed <<a href="mailto:lecielll@googlemail.com" target="_blank">lecielll@googlemail.com</a>> wrote:<u></u><u></u></p>
<p class="MsoNormal">Thank you for your input. I am going to run for another 15 ns to see if the little jumps vanish.<br>
<br>
Best,<u></u><u></u></p>
<div>
<div>
<p class="MsoNormal" style="margin-bottom: 12pt;"><u></u> <u></u></p>
<div>
<p class="MsoNormal">On Fri, Sep 9, 2011 at 9:16 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> wrote:<u></u><u></u></p>
<p class="MsoNormal"><br>
<br>
lina wrote:<u></u><u></u></p>
<div>
<blockquote style="border-width: medium medium medium 1pt; border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color rgb(204, 204, 204); padding: 0cm 0cm 0cm 6pt; margin-left: 4.8pt; margin-right: 0cm;">
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><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.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.<u></u><u></u></p>
</blockquote>
<p class="MsoNormal" style="margin-bottom: 12pt;"><u></u> <u></u></p>
</div>
<p class="MsoNormal">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.<u></u><u></u></p>
<div>
<blockquote style="border-width: medium medium medium 1pt; border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color rgb(204, 204, 204); padding: 0cm 0cm 0cm 6pt; margin-left: 4.8pt; margin-right: 0cm;">
<p class="MsoNormal" style="margin-bottom: 12pt;"><u></u> <u></u></p>
<p class="MsoNormal"><br>
You just need how to proper interpret your figures, truly understand what the "radial distribution" means.<br>
<u></u><u></u></p>
</blockquote>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<p class="MsoNormal">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.<u></u><u></u></p>
<div>
<p class="MsoNormal"><br>
<br>
-Justin<br>
<br>
-- <br>
========================================<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" target="_blank">
(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <u></u><u></u></p>
</div>
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