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] <javascript:>>: > > 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]<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/-/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.
