How can I calculated centre of mass rdf of aromatic ring from any peptide which containing aromatic ring using code and selecting atom of that ring?

[Python-hub-crypto]

For example, a peptide containing tryptophan which has an indole ring, Now how can I calculate the center of mass of that ring and then it's position to calculate the ring-to-ring center of mass rdf plot?

[orbeckst]

First you need to learn how to select the atoms that you're interested in — see Selections in the User Guide. This selection will give you an AtomGroup.

Then you can compute the center of mass of your AtomGroup with the AtomGroup.center_of_mass() method for each frame of the trajectory.

Once you have the coordinates of all centers that you want to calculate a RDF for, you need to write your own code because I am not aware of code in MDA that does it for you. You can look at the RDF code for atoms. In particular you need to first calculate all distances with code similar to

mdanalysis/package/MDAnalysis/analysis/rdf.py

Lines 269 to 272 in 7618e05

	pairs, dist = distances.capped_distance(self.g1.positions,
	self.g2.positions,
	self._maxrange,
	box=self._ts.dimensions)

and then histogram the distances

mdanalysis/package/MDAnalysis/analysis/rdf.py

Lines 287 to 288 in 7618e05

	count, _ = np.histogram(dist, **self.rdf_settings)
	self.results.count += count

This is going to be some work but should be do-able with the existing examples.