[gmx-users] radial distribution function

[Dallas Warren]

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.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Moeed
Sent: Friday, 16 September 2011 12:55 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] radial distribution function

Hello again,

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. :)

Moeed
On Sat, Sep 10, 2011 at 10:00 AM, Moeed <lecielll at googlemail.com<mailto:lecielll at googlemail.com>> wrote:
Thank you for your input. I am going to run for another 15 ns to see if the little jumps vanish.

Best,

On Fri, Sep 9, 2011 at 9:16 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:


lina wrote:



On Sat, Sep 10, 2011 at 3:35 AM, Moeed <lecielll at googlemail.com<mailto:lecielll at googlemail.com> <mailto:lecielll at googlemail.com<mailto:lecielll at googlemail.com>>> wrote:

   Dear users,

   I have created radial distribution function plot for Carbon atoms in
   a system containing polymer chains. I see some little jumps between
   first and second peak.
   I need your help to comment on how this behavior can be justified
   (or if the plot is wrong).

   g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx -b xxx
   Thank you in advance.


I think your figure is fine.

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.


You just need how to proper interpret your figures, truly understand what the "radial distribution" means.


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.


-Justin

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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