Hi everyone,<br><br>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). <br>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<br>
<br>I counted 23 residues that have area values > 1.3 nm2<br><br>I made an index file with one index group for each residue and on index group for "SOL_OW"<br>Then I ran g_rdf on my trajectory<br>g_rdf -s .tpr -f .xtc -n .ndx -o rdf.xvg -bin 0.02 -com<br>
I chose: reference group=the residue I want to analyze<br> group = "SOL_OW"<br><br>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<br>
My peak is at g(r)=0.7 and then it increases to g(r)=1<br><br>Does anyone have an idea why I have this kind of plot? Because I didn't find any answers in the mailing list.<br><br>Thank you,<br>Carla <br>