[gmx-users] radial distribution function

[Jan Henning Peters]

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.

Regards,

Jan


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
>