[gmx-users] Re: Strange form of RDF curve

Dr. Vitaly Chaban vvchaban at gmail.com
Thu Nov 15 20:28:29 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
> level,
> 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?

No. It is not 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
> surface).
> Thanks in advance,
> Igor Shchechkin

Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark

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