[gmx-users] Regarding calculation of coordination number

Dallas Warren dallas.warren at monash.edu
Wed Jul 19 01:42:52 CEST 2017

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.


Try searching the emailing list too, many times what you are asking
has been asked many times before
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,
> Ph.D Student
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