On 18 Oct 2012, at 11:49, Christoph Junghans wrote: > 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)
Great, updating now. > > - 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. WIll do that. Thank you for your help! > > Christoph > > 2012/10/17 Valentina <valentina_erast...@yahoo.co.uk>: >> 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 <valentina...@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 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/-/JWRcDYtHxR8J. >> >> 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. > -- You received this message because you are subscribed to the Google Groups "votca" group. 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