2012/10/17 Valentina <valentina_erast...@yahoo.co.uk>: > 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 > am I looking in the wrong place? Or shall I write ibi_bonded myself? You can get it via the buildutil
./build --dev csg-tutorials Christoph > > Thanks > V > > On Wednesday, October 17, 2012 5:19:34 PM UTC+1, Christoph Junghans wrote: >> >> 2012/10/17 Valentina <valentina...@yahoo.co.uk>: >> > 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 vo...@googlegroups.com. >> > To unsubscribe from this group, send email to >> > votca+un...@googlegroups.com. >> > 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 votca@googlegroups.com. > To unsubscribe from this group, send email to > votca+unsubscr...@googlegroups.com. > 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 post to this group, send email to votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
