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

shch406 shch406 at bpci.kiev.ua
Tue Nov 20 20:12:57 CET 2012

>I've never had an issue with similar commands.  Can you provide us with your 
>full g_rdf command line?  Have you verified that the index group for the 
>arginine residue is correct?  Can you provide a link to an image of the 
>resulting RDF?


My full g_rdf command line is as in my first post (except path and full
names of files):

/opt/software/gromacs/gromacs-4.5.3-intel/bin/g_rdf -f MT7w-145.trr -s
MT7w-145.tpr -n rs.ndx -o MT7w-145.RD-r205tipCOG.xvg -bin 0.05 -pbc -rdf

Atom numbers of the group in index file rs.ndx was taken from initial
conformation MT7w.gro file (3rd column) for NHH-NHH atoms of side chain tip
of 205 Arg.
These were verified to be correct.

RDF curve image inserted as rdf.bmp:


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