[gmx-users] Strange form of RDF curve

shch406 shch406 at bpci.kiev.ua
Thu Nov 15 18:53:22 CET 2012

Dear Gromacs users,

I tried g_rdf function and have obtained a strange result:
usually the RDF curve looks like relaxing oscillations around 1.0 constant
but in my case it appears to be oscillation around exponent going from 0.0
at zero distance to 1.0 at large distances.

Is the RDF obtained correct?

I used the command as follows:

g_rdf -f MT.trr -s MT.tpr -n rs.ndx -o MT.RD.xvg -bin 0.05 -pbc -rdf res_cog

where file MT.trr contains ~150 ps of equilibrated trajectory of 582 residue
protein in water;
The "reference group" was chosen "Water" and the  "1 group" was taken from
index file rs.ndx.
The latter group contains two tip NHH groups of charged arginine. (This
residue was inspected
on exposing to solvent and showed one of the largest solvent accessible

Thanks in advance,
Igor Shchechkin

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