GROMACS version: 2018.1
GROMACS modification: Yes/No
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I simulated a reverse micellar system where Isopropyl myristate (IPM) has been used as a bulk oil phase. Sodium AOT surfactant molecule (AOT anion and sodium cation) forms the interface while water molecules exist inside the polar core wrapped by sodium AOT molecules. I ran the simulation for 70 ns and tried to analyze the last 20ns window to plot the g(r) of oxygen atom of water, around the S atom of AOT molecules. Then I found that the peak value of g(r) comes to near 40 while it decreases to 0.4 along the distance in X axis.
Thus, to plot the RDF between the S atom of AOT anions and oxygen atom (OW) of water molecules, I prepared an index file with:
gmx make_ndx -f .tpr -o index.ndx
→ a S | a OW
Later I did plot the RDF of OW atoms as ‘sel’ around S atom as ‘ref’ with the command:
gmx rdf -s .tpr -f .xtc -n index.ndx -o ref.xvg
Here the g(r) value becomes at a long distance while it’s supposed to be one!
So where am I making mistakes? Is there any possibility that the graphs were not normalized as the g(r) values are extremely high in some cases.