[gmx-users]site-site radial distribution function

Payman Pirzadeh ppirzade at ucalgary.ca
Sat Oct 30 00:52:33 CEST 2010


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?







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