Using "-surf" means the results will not be normalised i.e, "-norm" can't be used. That is why it is giving such high values. 

Ok, thanks, Sayantan. 

That leaves me with trying to find an actually Surface Distribution Function.

What would be the best way to quantify how much water is around a side chain? 

Thanks

Anthony 

Sounds like what you want is a coordination number, e.g. gmx rdf -cn or just integrate the RDF itself. The -surf option simply constructs a surface around the solute and uses that as the RDF reference rather than the individual atomic coordinates. Maybe what you're after is a spatial distribution function, e.g. gmx spatial? But that's sort of a qualitative assessment because the only output is a cube file with the spatial occupancies.

Hi Justin,

Thanks for your post. It was extremely useful. I just took a closer look at the rdf -h:

"Option -cn produces the cumulative number RDF, i.e. the average number of particles within a distance r." I'll give that a try. Plus, thanks for raising my awareness regarding gmx spatial, I'll look into that. 

Thanks again.

hi Anthony,

if you can, try writing a code just using the trajectory. as it can be customised, you can find out the exact reason for such anomalous values.

thanks

Hi Justin, 

I see what you mean with qualitative information. I've had a play around with spatial and following the necessary instructions I have the water occupancy in a cube file around two amino acids (iso via VMD attached). Any idea what defines the occupancy? I assume it will correlate with the peaks in the RDF? 

I'm looking at interstitial water content in collagen, pre and post glycation of two of its residues. I will never see the RDF reach bulk as my system replicates collagen molecules via PBCs.