2016-01-25 9:14 GMT-07:00 Chang Woon Jang <[email protected]>: > Dear Votca Users, > > > I am trying to run ibi with my own polymer system to derive non-bonded > potentials. > > I am trying to look at inverse.log file but I do not figure out what the > problem is. Would you please give me some advice? > > I set for A and D beads interaction in setting.xml file below, and my A-D > target rdf from 0 to 2 obtained from csg_stat command. Step size is 0.01 and > the rdf looks fine for me. > > <non-bonded> > <!-- name of the interaction --> > <name>A-D</name> > <!-- types involved in this interaction --> > <type1>A</type1> > <type2>D</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0</min> Why 0? I am sure your rdf isn't well-defined for 0. Pick a min which slightly before the 1st peak. If you really want to use min=0, ensure all points in CG-CG.A-D.dist.tgt before the 1st peaks starts are 0.
> <max>2.0</max> > <step>0.01</step> > > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>CG-CG.A-D.dist.tgt</target> > <!-- update cycles --> > <do_potential>0 0 0 0 0 0 1</do_potential> > <!-- additional post processing of dU before added to potential --> > <post_update></post_update> > <!-- additional post processing of U after dU added to potential --> > <post_add>convergence</post_add> > <!-- inverse monte carlo specific stuff --> > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_A_D.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > > The error message inverse.log is attached. In short, it says that > > > > Running subscript 'dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435 > --min 1e-10 A-D.dist.tgt A-D.pot.new.raw.R6h' (from tags dist invert) dir > /home/chang/PACKAGE/votca/share/votca/scripts/inverse > Only 3 points are valid after Boltzmann inversion from file 'A-D.dist.tgt', > please check if your distribution is a valid dist. Have a look at A-D.dist.tgt in step_000 and look for the points having "i" in third column. Usually that error is triggered if there is a value bigger than 10^-10 before the first peak of the rdf and votca picks it up as a valid point. These points cannot be cropped automatically, because something you want to use them. Christoph > > Callstack: > /home/chang/PACKAGE/votca/share/votca/scripts/inverse/inverse.sh - > linenumber 156 > do_external - linenumber 176 in > /home/chang/PACKAGE/votca/share/votca/scripts/inverse/functions_common.sh > > /home/chang/PACKAGE/votca/share/votca/scripts/inverse/prepare_generic.sh - > linenumber 31 > for_all - linenumber 22 (see 'csg_call --cat function for_all') > do_external - linenumber 19 (see 'csg_call --cat > function do_external') > > /home/chang/PACKAGE/votca/share/votca/scripts/inverse/prepare_generic_single.sh > - linenumber 64 > do_external - linenumber 22 (see 'csg_call --cat > function do_external') > die - linenumber 2 (see 'csg_call --cat > function die') > ############################################################################################################################################################### > # > # > # ERROR: > # > # do_external: subscript > # > # > /home/chang/PACKAGE/votca/share/votca/scripts/inverse/dist_boltzmann_invert.pl > --type non-bonded --kbT 2.49435 --min 1e-10 A-D.dist.tgt A-D.pot.new.raw.R6h > # > # (from tags dist invert) failed > # > # For details see the logfile > /home/chang/PROJECT/2_CG_DGEBA_JD230/2_CG_DGEBA_JD230_MIDDEL_GENERIC/4_Lammps_TEST/2_IBI/inverse.log > # > # > # > ############################################################################################################################################################### > > > Thank you very much. > > > Best regards, > Changwoon Jang, > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
