[gmx-users] Regarding calculation of coordination number

[Dallas Warren]

2) to calculate it yourself you integrate the area under the g(r)
curve between the two minima and multiple that by the atomic density.
Easy to do, even can do in a spreadsheet such as Excel.

https://en.wikibooks.org/wiki/Molecular_Simulation/Radial_Distribution_Functions#Coordination_Numbers

Try searching the emailing list too, many times what you are asking
has been asked many times before
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 19 July 2017 at 02:13, Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
> Hello,
> i have calculated the radial distribution function through the commands as:-
> gmx rdf -f ab.ttr -s ab.tpr -n ab.ndx -o rdf_ab.xvg -ref x -sel y -cn
> cn_ab.xvg
>
> 1] my doubt is tht whether -cn option is calculating the co-ordination
> number ie., running coordination number [N(r)] or just the coordination
> number [CN]..??
> Because when i compare the 1st minima of rdf value to the corresponding
> coordination number tht i have got by -cn flag is not matching.. i am
> getting very less coordination number even with the corresponding
> second/third minima value of rdf also..
> can anybody help........??
> 2] And if want to calculate coordination number by the formula, how can i
> do tht.?? should i manually integrate and calculate the values till 1st
> minima or do i need to write a small code for tht.?? how could i solve this
> issue..??
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
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