2013/7/25 <[email protected]>: > 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 You have to make the script executable: $ chmod u+x my_rdf.sh
> > 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]>: >> > 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 >> >> >> >> >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to [email protected]. >> > To post to this group, send email to [email protected]. >> > Visit this group at http://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/groups/opt_out. >> > >> > >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. > > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
