[gmx-users] g_sas and g_rdf

Carla Jamous carlajamous at gmail.com
Mon Nov 15 15:16:41 CET 2010

Hi everyone,

I'm trying to look at the radial distribution function of water around the
surface of my protein. For that, I calculated the surface area per residue
(g_sas -or).
Since I didn't find in the litterature any criteria to choose a minimum area
value to count a residue as a a surface residue, I chose to analyze the
residues that have an area value > 1.3 nm2

I counted 23 residues that have area values > 1.3 nm2

I made an index file with one index group for each residue and on index
group for "SOL_OW"
Then I ran g_rdf on my trajectory
g_rdf -s .tpr -f .xtc -n .ndx -o rdf.xvg -bin  0.02 -com
I chose: reference group=the residue I want to analyze
             group = "SOL_OW"

even though I'm analyzing the residues that have large surface area values,
my RDF plot doesn't look like what I was execting: it means an RDF plot with
a peak at g(r)=2 or 3 then a decrease in g(r) and finally a g(r)=1
My peak is at g(r)=0.7 and then it increases to g(r)=1

Does anyone have an idea why I have this kind of plot? Because I didn't find
any answers in the mailing list.

Thank you,
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