No, I have not run hexane ibi_bonded. I have not realised there is a tutorial for it. I may looking in wrong place - but I dont seem to find it in votca-csg-tutorials-1.2.3.tar.gz<http://votca.googlecode.com/files/votca-csg-tutorials-1.2.3.tar.gz>
am I looking in the wrong place? Or shall I write ibi_bonded myself? Thanks V On Wednesday, October 17, 2012 5:19:34 PM UTC+1, Christoph Junghans wrote: > > 2012/10/17 Valentina <[email protected] <javascript:>>: > > Done, thank you. Now I am stuck with: > > > > Using given table CC.pot.in for CC > > > ################################################################################################################################ > > > > # > > # > > # ERROR: > > # > > # potential_extrapolate.sh: please specify add potential type (--type > > options) from: non-bonded bond thermforce angle dihedral # > > # For details see the logfile /home/valentina/CG/inverse.log > > # > > # > > # > > > ################################################################################################################################ > > > > Terminated > Something is not right. Have you tried to run the hexane ibi_bonded > potential? > Just in case to check your installation. > > Can you send me the last 100 lines of inverse.log? > > Christoph > > > > > > I am not sure where to add this. I have added like this to every > > interaction: > > > > <bonded> > > <name>CC</name> > > <min>0</min> > > <max>4</max> > > <step>0.01</step> > > > > <inverse> > > <target>CC.dist.tgt</target> > > <do_potential>1 0 0 0 </do_potential> > > > > <post_update>scale</post_update> > > <post_update_options> > > <scale>0.1</scale> > > </post_update_options> > > > > <post_update>pressure</post_update> > > <post_update_options> > > <pressure> > > <type>simple</type> > > <do> 1 0 0 0</do> > > <simple> > > <scale>0.0001</scale> > > </simple> > > </pressure> > > </post_update_options> > > > > <post_update_options> > > <extrapolate> --type bond </extrapolate> > > </post_update_options> > > > > <post_add></post_add> > > <gromacs> > > <table>table_b1.xvg</table> > > </gromacs> > > </inverse> > > </bonded> > > > > But it doesn't seem to pick up the input. > > > > Also the programm asked me to provide CC.pot.in > > I was not sure what is this potential, so I provided CC-bond.pot.ib (the > > output from csg_boltzmann) - is this right? > > > > Thank you very much, > > V > > > > > > > > > > > > On Friday, September 28, 2012 2:07:44 PM UTC+1, Valentina wrote: > >> > >> Hello! > >> > >> I am a little confused here. > >> > >> I have read somewhere that Votca 1.3 (? I thought latest version is > 1.2.3) > >> supports IBI for bonded - is this right? > >> > >> If so, how do I implement it? I have attatched my settings file (saved > in > >> .odt,but used as .xml on the machine). This doesn't seem to do more > then > >> fitting the nonbonded C-C potential. Am I missing something? > >> > >> Many thanks! > >> Valentina > > > > -- > > You received this message because you are subscribed to the Google > Groups > > "votca" group. > > To view this discussion on the web visit > > https://groups.google.com/d/msg/votca/-/uahanZ2h6ccJ. > > > > To post to this group, send email to [email protected]<javascript:>. > > > To unsubscribe from this group, send email to > > [email protected] <javascript:>. > > For more options, visit this group at > > http://groups.google.com/group/votca?hl=en. > > > > -- > Christoph Junghans > Web: http://www.compphys.de > -- You received this message because you are subscribed to the Google Groups "votca" group. To view this discussion on the web visit https://groups.google.com/d/msg/votca/-/MN8M51uySo0J. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
