It works, absolutely amazing! Thank you a lot!!!!!!!!!!!! On Thursday, July 25, 2013 4:40:37 PM UTC+1, Christoph Junghans wrote: > > 2013/7/25 <[email protected] <javascript:>>: > > 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]: > >> >> > >> >> 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] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > 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 >
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