Hi Valentina, I had another look at your input files and found the problem.
- The name you give a bonded interaction in the mapping file has to be the same as the name of the interaction in the settings file. That is how the type detection works. (There was a check missing in the code, which lead to error in the extrapolation, I fixed that. You can use "./build -du csg" to get the update) - In your mapping file you have defined the bonds and angle, but the definition of the beads is missing. Have a look the hexane example, in principle you have to create a 1:1 map. And try to run csg_stat with --cg option once by hand to see if the distributions are calculated correctly. Christoph 2012/10/17 Valentina <[email protected]>: > Ok, great. I will try the tutorial and see where I have gone wrong. > > > On Wednesday, October 17, 2012 6:15:02 PM UTC+1, Christoph Junghans wrote: >> >> 2012/10/17 Valentina <[email protected]>: >> > 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 <[email protected]>: >> >> > 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]. >> >> > 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. >> >> >> >> >> >> >> >> -- >> >> 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. >> >> >> >> -- >> 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/-/JWRcDYtHxR8J. > > 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. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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