[gmx-users] RDF - water and protein

Steven Neumann s.neumann08 at gmail.com
Mon May 13 16:01:05 CEST 2013

Dear Gmx Users,

I run long simulation of my protein with 50 small molecules in water.
I calculated the RDF (Protein - Water) using -surf mol and -rdf mol_com.
Please, take a look at my plot:


Could you please, explain me why the second peak is so high? Shall I use
option -nopbc ?
How can I obtain the density [kg/m3] versus the distance? I wish to compare
it with RDF of Protein-Ligands so wish to use some normalization for them
to be comparable - peaks will be visible.


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