On Tue, May 8, 2018 at 8:15 AM, <jjbm.resea...@gmail.com> wrote: > Dear all, > > I am learning to use VOTCA with LAMMPS and the IBI method, and have > successfully tested the spce example and coarse-grained a monoatomic > material. > > Now, I am trying to make a dodecane chain model of structure A-B-B-A, and > using the hexane example as a reference to create the setting, mapping and > topology files. The LAMMPS files for the coarse-grained dodecane have been > tested and work fine. Actually, I am getting errors just after the LAMMPS > run of the first iteration. These errors are related to the topology file > topol.top. In first place, the error was related to the absence of this file > (not needed in the monoatomic case), and now that I am using an adaptation > of the hexane's topol.top file, it is the format to blame according to > inverse.log: > > Calculating rdfs with csg_stat using 8 tasks > Running critical command 'csg_stat --nt 8 --options > /home/jjbm/Documents/Molecules/Topologies/SimpleExamples/Dodecane/CG_Dodecane/cg_450K/test_nononbonded/settings.xml > --top topol.top --trj traj.dump --begin 0 --$ > begin to calculate distribution functions > # of bonded interactions: 0 > # of non-bonded interactions: 3 > an error occurred: > input format not supported: topol.top > > Callstack: > ~/share/votca/scripts/inverse/inverse.sh - linenumber 264 > do_external - linenumber 176 in > ~/share/votca/scripts/inverse/functions_common.sh > ~/share/votca/scripts/inverse/update_ibi.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') > ~/share/votca/scripts/inverse/calc_rdf_generic.sh - > linenumber 79 > 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 /test_nononbonded/settings.xml --top > topol.top --trj traj.dump --begin 0 --first-frame 0$ > # For details see the logfile /test_nononbonded/inverse.log > $ > # > $ > ####################################################################################################################################################################################################################$ > die: (called from 9953) CSG_MASTER_PID is 6366 > die: pids to kill: 0 > > Attached are the three files corresponding to this molecule. Since I have > never used GROMACS, I am not sure what I am doing wrong there. Any help? Yeah, you have to run convert the top file into a binary topology file tpr first using "gmx grompp". VOTCA only supports reading the tpr file, but not the top file as the latter doesn't contain the full information.
Christoph > > Thanks in advance, > Kind regards > > -- > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
