Hi Marcelo,
The total number of water molecules within a certain distance from the central atom is the area under the curve at that distance, as given in the ‘intrude’ file. In your case, since you gave this file the same as the ‘outfilename' (radial.dat), it would be the data in the 3rd column in the file.
To plot that with xmgrace you need to open it with the -nxy flag:
]$ xmgrace -nxy radial.dat
HTH,
—
Gustavo Seabra.
> Em 23 de fev de 2018, à(s) 15:39, Marcelo Andrade Chagas <andrade.mchagas.gmail.com> escreveu:
>
> Dear from the AMBER list,
>
> I am getting the RDF from a specific atom of the active site of
> a protein.
>
> my simulation in the field of production is 800 ns
>
> I'm using the following script with cpptraj and getting the RDF profile
> below:
> ___________________________________________________________________________
>
> trajin estagio_14.mdcrd
> autoimage
> radial radial.dat 0.3 10.0 :332.H1 :WAT.O&!(:1-332.O) density 0.022 intrdf
> radial.dat
>
> ___________________________________________________________________________
>
> [image: Imagem intercalada 1]
>
>
> My question is: how do I define the number of water molecules in
> each layer of solvation obtained on average, for example?
>
> Best regards,
>
> Marcelo
>
> Marcelo Andrade Chagas, MSc
> (PhD student)
> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> * http://lqcmm.qui.ufmg.br/
> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> Tel:(31)3409-5776
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Received on Fri Feb 23 2018 - 11:30:03 PST
