[gmx-users] radial distribution function

Jan Henning Peters jan.henning.peters at fu-berlin.de
Sun Jul 1 20:23:28 CEST 2018

Dear Azadeh,

if you used gmx rdf for the calculation, you likely calculated the rdf 
between the atoms of the CNT and the atoms of your drug molecules. If a 
drug molecule is 1.5 nm from the centre of a CNT which has 1 nm radius, 
it approximately 0.5 nm from the closest atom of the CNT, which would 
explain the peak at this distance.



On 01/07/2018 20:05, kordzadeh at aut.ac.ir wrote:
> ​​​Hi all
> I want to investigate adsorption drug on CNT,, the radius of CNT is 1 nm, RDF and distance of each drug around CNT were calculated, but I couldn't attach these picture in this email,
> I saw, all drugs adsorbed on CNT surface at distance 1.5 nm, but I couldn't understand why the intense peak of RDF is less than 1 nm, I can't explain it, itense peak at 0.5 nm tells that  drugs are in the internal space of CNT because radius of CNT is 1 nm and intense peak is less than 1nm,
> is my explanation wrong?
> please help me
> what is the interpretation of first peak and second peak
> Thanks
> Regards
> Azadeh

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