Hello, I successfully extracted bonded parametrs for my protein CG model based on the atomistic simulation. In my CG I have 6 different beads, each corresponding to one amino acid. I want to calculate cumulative RDF (radial distribution functions) between them as an input to IBI. I group them in 6 beads running RDF... however I feel I should exclude groups which are really close as it will influence RDF too much and the potential - 1-3 interactions should be omitted, On the other hand groups I want to exclude will interact with given group which is more far away. is there any rule for exclusions in these case? I will appreciate your help.
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