[gmx-users] radial distribution function

Justin A. Lemkul jalemkul at vt.edu
Sat Sep 10 06:16:46 CEST 2011

lina wrote:
> On Sat, Sep 10, 2011 at 3:35 AM, Moeed <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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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