I am trying to calculate the rdf of water molecules present inside the Carbon nanotube.
I tried to do the indexing first using gromacs tool gmx selection. But when it comes to calculating rdf, I can only opt for one of the frames as available in the index file created using the gmx selection of water molecules inside of the tube.
I need help regarding the rdf calculation of water molecules present inside of the tube using code or gromacs if possible........
I hope someone can answer this issue and guide me in the direction to either write a code to do the calculation.
Thanks in advance.
dear Anupama Sharma ;
in my opinion, you have to calculate the potential of mean force (PMF) inside the nanotubes to understand the amount of energy barrier that exists inside the nanotube [30]. Water molecules have to overcome this energy barrier to move through the nanotube. The potential of mean force is calculated as follows:
PMF = (−kBT) ln g(x)
where;
g(x) is the radial distribution function(RDF)
kB the Boltzmann constant
T the thermodynamic temperature
As detailed in the following references;
- https://core.ac.uk/download/pdf/268797275.pdf
Article Deformation Effect on Water Transport through Nanotubes
Dear Anupama Sharma
The index file is not a frame , it is the number of molecules and does not show the position of molecules.
You should analyze md trajectory with RDF , you have the radius of carbon nanotube if the first peak of RDF lower than CNT radius, it means the water molecules were trapped in CNT
I also used this method to find encapsulation of drug molecules in CNT
you could see my paper
https://www.sciencedirect.com/science/article/abs/pii/S1093326318306685
hope it helps
Thanks for the reply Azadeh Kordzadeh, Mahmood H. M. .
I will definitely look into the article.
Also, index file is not a frame, I know this part it contains the residue number corresponding to the molecule, but when we use gmx selection ....... It does the dynamic selection as it selects molecules presents in a location that has been specified and writes its residue number in .ndx file frame wise.
And when I use that index file to calculate the rdf , it gives option to select the frame that contains molecules.
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