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

[André Farias de Moura]

there is nothing wrong about the rdf, except for some noise that would
disappear
for a longer simulation. the fact that you have a region with rdf values
below 1 is
just a diagnosis for the excluded volume in your system (the protein is dry
inside,
so the volume occupied by the protein do not contribute to the hydration).

cheers

Andre

On Tue, Nov 20, 2012 at 5:12 PM, shch406 <shch406 at bpci.kiev.ua> wrote:

> >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?
>
> >-Justin
>
> 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
> res_cog
>
> 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:
> <http://gromacs.5086.n6.nabble.com/file/n5003142/rdf.bmp>
>
> Igor
>
>
>
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090