[gmx-users] Surface Distribution Function in gromacs

[Nash, Anthony]

Hi all,

A very quick sanity check question regarding one of the gromacs analysis
tools. 

Does the -surf option in gmx_d rdf (or rdf_d in 5.0.#) yield a Surface
Distribution Function plot I.e., related to the average density of water
molecules around the protein surface? I¹ve tried, and I get a plot not too
dissimilar to an RDF but with values around 0 to 300. I¹m not exactly sure
what the value on the y-xis is. There is no description in the .xvg file.

I would just like clarity that an SDF is in fact the same as this
description in the help, ³To compute the RDF with respect to the closest
position in a set in -ref instead, use -surf: if set, then -ref is
partitioned into sets based on the value of -surf, and the closest
position in each set is used."

Thanks
Anthony