Hello,

I have two questions about using g_rdf:

 

1.       Is it meaningful to calculate the radial distribution of water
molecules around a single atom of a surface residue, e.g. dangling OG1
oxygen of Threonine? (Does g_rdf takes care of the protein presence and the
excluded volume?)

2.       How will the RDF be calculated in a heterogeneous system? For
instance, if you have protein in a solvent near a solvent's crystal's
surface? What is considered as the bulk density of the solvent? Whole box?

Thanks.

 

Paymon

 

 

 

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