[gmx-users] Strange form of RDF curve

David van der Spoel spoel at xray.bmc.uu.se
Fri Nov 16 09:33:25 CET 2012

On 2012-11-15 18:53, shch406 wrote:
> 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?
> 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
I think you need to switch the arguments, first side chain then water.
> --
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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