Hi, 2012/10/24 Valentina <valentina_erast...@yahoo.co.uk>: > > Hello, > > I am having a problem, I cannot identify how to solve. > > I am doing IBI of bonded interactions and so I get an error. > > There must be smth wrong between cg-mapping.xml and topol.top files, but I > cannot spot what. I also get error of same type if I run > > csg_dump as a check. Could the identifier in the mapping xml file be wrong? The identifier is the name from the [ moleculetype ] block in topol.top
If you have multiple molecule type in your system, you will need a mapping file for each them, but I haven't added multiple type support to csg_inverse. It is not hard to add. Christoph > > Thank you! > > > > List of molecules: > -------------------------------------- > WARNING: unknown molecule "DCG" with id 0 in topology > Reading frame 0 time 0.000 molecule will not be mapped to CG > representation > Check weather a mapping file for all molecule exists, was specified in --cg > separated by ; and the ident tag in xml-file matches the molecule name > -------------------------------------- > > Reading frame 50 time 10.000 an error occurred: > Topology does not have beads of type "C" > This was specified in type1 of interaction "C-C" > > Callstack: > /share/apps/votca/share/votca/scripts/inverse/inverse.sh - linenumber 252 > > do_external - linenumber 170 in > /share/apps/votca/share/votca/scripts/inverse/functions_common.sh > /share/apps/votca/share/votca/scripts/inverse/update_ibi.sh - > linenumber 31 > > for_all - linenumber 17 (see 'csg_call --cat function for_all') > do_external - linenumber 18 (see 'csg_call --cat > function do_external') > > /share/apps/votca/share/votca/scripts/inverse/calc_rdf_generic.sh - > linenumber 71 > critical - linenumber 4 (see 'csg_call --cat > function critical') > > die - linenumber 2 (see 'csg_call --cat > function die') > ######################################################################################################################################################################################### > > # > # > # ERROR: > # > # critical: 'csg_stat --nt 8 --options /home/valentina/CG/GAS/settings.xml > --top topol.tpr --trj traj.xtc --begin 10 --first-frame 0 --cg > /home/valentina/CG/GAS/cg-mapping.xml' failed # > # For details see the logfile /home/valentina/CG/GAS/inverse.log > # > # > # > ######################################################################################################################################################################################### > die: (called from 7667) CSG_MASTER_PID is 7125 > > die: pids to kill: 0 > > > > 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/-/6pOJ6qExAD4J. > > 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.
