[AMBER] RDF vs, Coordination numbers

From: Damiano Spadoni via AMBER <amber.ambermd.org>
Date: Thu, 30 Jun 2022 16:46:51 +0000

Dear AMBER maniacs,

I am simulating a box containing a protein P in a mix of solvents S1 and S2 in presence of an electrolyte EL using AMBER20 on GPU acceleration.
I want to calculate the radial distribution function of EL molecules around P and their relative coordination numbers.
When I use the following command in cpptraj:

radial out OutputFileName.dat 0.1 15 :EL_ResidueMask :P_ResidueMask noimage volume bymol1 byres2

it retrieves what I think is the RDF of EL molecules around P calculated by using the density of the whole box in each frame, taking into account EL molecules and protein residues but please correct me if I am wrong. When plotted, the RDF looks like the green curve in the attached image.
When I use the command:

radial out OutputFileName.dat 0.1 15 :EL_ResidueMask :P_ResidueMask noimage volume center1 center2

I get what I think are the coordination numbers between EL molecules and P by using the density of the whole box in each frame, considering the interaction between the center of both EL molecules and P but the values range seems to be quite small to me as if the 1st solvation shell for EL was recorded at 6nm distance from P and it accounted for 1 molecule (represented in purple in the image). I didn't use any normalisation so I'd expected similar values. Is this wrong to think?
Or have I just swapped the two commands?

I also wanted to know that since from the theory we know that the relation between RDF and coordination numbers between two particles a and b as a function of the distance r is:

N{ab}(r) = rho G{ab}(r)

where rho is the density and G(r) the RDF, what is the keyword that differentiate between RDF to coordination numbers in the commands I used?

Is it right to use the "volume" keyword if I want to calculate the properties of the electrolyte in the mix of solvents or should I have used "density" along with the value for density retrieved by
0.6022/MEL ‚Äč(with MEL the mass of an EL molecule)?

Kind regards,

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(image/png attachment: RDFvsCN-1.png)

Received on Thu Aug 04 2022 - 13:33:56 PDT
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