I did what you have written copying the file from 2011 to the "scripts"
folder and I got the error and creating csg_table. I also added option
-fade 2.0 in xml file gromacs.g_rdf.opts and when running:
#
ERROR:
#
# do_external: subscript
/home/ps/ps-fs2/jkm210/Polyglycine/CHANDLER/IBI_METHOD/WCA_probeb4_IBI/scripts/my_rdf.sh
(from tags rdf gromacs) failed #
WORK/IBI_METHOD/WCA_probeb4_IBI/scripts/my_rdf.sh: Permission denied
Would you suggest something please?
Steven
On Thursday, July 25, 2013 3:55:08 PM UTC+1, Christoph Junghans wrote:
>
> 2013/7/25 <[email protected] <javascript:>>:
> > And how g_rdf tool of gromacs will know which groups to use from
> index.ndx ?
> That was one of the reason to deprecate g_rdf and make csg_stat the
> default. VOTCA uses types not energy groups.
>
> Back in 2011, we used the following script:
> <
> https://code.google.com/p/votca/source/browse/share/scripts/inverse/calc_rdf_gromacs.sh?repo=csg&name=a3e6095e3ee6>
>
>
> This could serve as basis for your myrdf.sh
> >
> > Steven
> >
> >
> > On Monday, July 15, 2013 12:02:00 PM UTC+1, [email protected] wrote:
> >>
> >> Dear Votca Users,
> >>
> >> I have to issues with IBI:
> >>
> >> 1) I took one my ditributions and calculated on my own potential W=
> -kBT
> >> ln(RDF) and I got different potential than Votca provide me. For
> instance
> >> lets calculate the potential minimum for the distribution maximum of
> 162.
> >> Pot = -.249435*ln(164) = -12.69. The minimum of Votca potential
> corresponds
> >> to approximately -16 kJ/mol. Where I missed something? is it somehow
> >> normalized?
> >>
> >> 2) After 1st iteration my distribution was much higher than the target
> one
> >> so I guess the potential should decrease but apparently the new
> potential
> >> has deeper minima so the next distribution has a even higer
> distribution.
> >> Could anyone please explain me this?
> >>
> >> Steven
> >>
> >>
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>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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