For a more verbose log see: inverse.log csg_get_property: No value for 'cg.inverse.mpi.tasks' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.mpi.tasks' csg_get_property: No value for 'cg.inverse.mpi.cmd' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.mpi.cmd' csg_get_property: No value for 'cg.inverse.parallel.tasks' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.parallel.tasks' csg_get_property: No value for 'cg.inverse.parallel.cmd' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.parallel.cmd' csg_get_property: No value for 'cg.inverse.gromacs.mdrun.bin' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.mdrun.bin' csg_get_property: No value for 'cg.inverse.espresso.bin' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.espresso.bin' csg_get_property: No value for 'cg.inverse.scriptdir' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.scriptdir' csg_get_property: No value for 'cg.inverse.gromacs.grompp.topol' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.grompp.topol' csg_get_property: No value for 'cg.inverse.gromacs.grompp.index' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.grompp.index' csg_get_property: No value for 'cg.inverse.gromacs.g_rdf.topol' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.g_rdf.topol' csg_get_property: No value for 'cg.inverse.convergence_check' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.convergence_check' csg_get_property: No value for 'cg.inverse.convergence_check_options.name_glob' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.convergence_check_options.name_glob' csg_get_property: No value for 'cg.inverse.convergence_check_options.limit' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.convergence_check_options.limit' csg_get_property: No value for 'cg.inverse.espresso.table_end' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.espresso.table_end' csg_get_property: No value for 'cg.inverse.gromacs.traj_type' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.traj_type' csg_get_property: No value for 'cg.inverse.gromacs.topol_out' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.topol_out' csg_get_property: No value for 'cg.inverse.espresso.blockfile' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.espresso.blockfile' csg_get_property: No value for 'cg.inverse.espresso.blockfile_out' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.espresso.blockfile_out' csg_get_property: No value for 'cg.inverse.espresso.n_steps' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.espresso.n_steps' csg_get_property: No value for 'cg.inverse.espresso.exclusions' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.espresso.exclusions' csg_get_property: No value for 'cg.inverse.espresso.debug' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.espresso.debug' csg_get_property: No value for 'cg.inverse.espresso.n_snapshots' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.espresso.n_snapshots' csg_get_property: No value for 'cg.non-bonded.inverse.espresso.index1' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.non-bonded.inverse.espresso.index1' csg_get_property: No value for 'cg.non-bonded.inverse.espresso.index2' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.non-bonded.inverse.espresso.index2' csg_get_property: No value for 'cg.inverse.espresso.success' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.espresso.success' csg_get_property: No value for 'cg.inverse.espresso.scriptdir' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.espresso.scriptdir' csg_get_property: No value for 'cg.non-bonded.inverse.post_update_options.kbibi.type' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.non-bonded.inverse.post_update_options.kbibi.type' csg_get_property: No value for 'cg.inverse.imc.numpy.bin' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.imc.numpy.bin' csg_get_property: No value for 'cg.inverse.imc.octave.bin' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.imc.octave.bin' csg_get_property: No value for 'cg.inverse.imc.matlab.bin' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.imc.matlab.bin' csg_get_property: No value for 'cg.inverse.imc.solver' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.imc.solver' csg_get_property: No value for 'cg.non-bonded.inverse.imc.reg' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.non-bonded.inverse.imc.reg' Sim started Wed Aug 5 18:11:55 IST 2020 We are doing Method: ibi csg_get_property: No value for 'cg.inverse.scriptpath' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.scriptpath' We are using Sim Program: gromacs csg_get_property: No value for 'cg.inverse.gromacs.gmxrc' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.gmxrc' #The order in which scripts get called #CSGSHARE is /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse #From: /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse/csg_table tag file tag_file.sh dummy dummy dummy.sh functions common functions_common.sh csg master inverse.sh prepare ibi prepare_generic.sh prepare imc prepare_imc.sh prepare generic prepare_generic.sh prepare optimizer prepare_optimizer.sh prepare re prepare_re.sh prepare_single ibi prepare_generic_single.sh prepare_single imc prepare_generic_single.sh prepare_single optimizer prepare_optimizer_single.sh initstep ibi initialize_step_generic.sh initstep imc initialize_step_generic.sh initstep optimizer initialize_step_optimizer.sh initstep re initialize_step_re.sh add_pot ibi add_pot_generic.sh add_pot imc add_pot_generic.sh add_pot optimizer dummy.sh add_pot re dummy.sh pre_update ibi dummy.sh pre_update imc dummy.sh pre_update optimizer dummy.sh pre_update re pre_update_re.sh post_update ibi post_update_generic.sh post_update imc post_update_generic.sh post_update optimizer dummy.sh post_update re post_update_generic.sh post_update_single ibi post_update_generic_single.sh post_update_single imc post_update_generic_single.sh post_update_single re post_update_re_single.sh postupd scale postupd_scale.sh postupd pressure postupd_pressure.sh postupd lj postupd_addlj.sh postupd splinesmooth postupd_splinesmooth.sh postupd smooth postupd_smooth.sh postupd shift postadd_shift.sh postupd dummy postadd_dummy.sh postupd tag tag_file.sh postupd extrapolate postupd_extrapolate.sh postupd kbibi postupd_kbibi_correction.sh postupd cibi postupd_cibi_correction.sh post add post_add.sh post add_single post_add_single.sh postadd tag tag_file.sh postadd dummy postadd_dummy.sh postadd copyback postadd_copyback.sh postadd compress postadd_compress.sh postadd convergence postadd_convergence.sh postadd acc_convergence postadd_acc_convergence.sh postadd shift postadd_shift.sh postadd overwrite postadd_overwrite.sh postadd plot postadd_plot.sh postadd average postadd_average.sh convergence_check default convergence_check_default.sh resample target resample_target.sh update ibi update_ibi.sh update ibi_single update_ibi_single.sh update ibi_pot update_ibi_pot.pl update imc update_imc.sh update imc_single update_imc_single.sh optimizer prepare_state optimizer_prepare_state.sh optimizer parameters_to_potential optimizer_parameters_to_potential.sh optimizer state_to_potentials optimizer_state_to_potentials.sh optimizer state_to_mapping optimizer_state_to_mapping.sh update optimizer update_optimizer.sh update optimizer_single update_optimizer_single.sh optimizer_target rdf optimizer_target_rdf.sh optimizer_target density optimizer_target_density.sh optimizer_target pressure optimizer_target_pressure.sh simplex precede_state simplex_downhill_processor.pl cma precede_state cma_processor.py update re update_re.sh calc target_rdf calc_target_rdf_generic.sh pressure_cor simple pressure_cor_simple.pl pressure_cor wjk pressure_cor_wjk.pl compute_lj 12_6 lj_126.pl kbibi ramp_correction kbibi_ramp_correction.pl calc kbint calc_kbint.sh table add add_POT.pl table integrate table_integrate.pl table extrapolate table_extrapolate.pl table merge merge_tables.pl table smooth table_smooth.pl table linearop table_linearop.pl table dummy table_dummy.sh table get_value table_get_value.pl table switch_border table_switch_border.pl table compare table_combine.pl --die --op = table combine table_combine.pl table average table_average.sh table scale table_scale.pl table change_flag table_change_flag.sh table functional table_functional.sh potential extrapolate potential_extrapolate.sh potential shift potential_shift.pl convert_potential tab table_to_tab.pl dist adjust dist_adjust.pl dist invert dist_boltzmann_invert.pl tables jackknife tables_jackknife.pl initstep gromacs initialize_step_genericsim.sh run gromacs run_gromacs.sh clean gromacs clean_generic.sh presimulation gromacs run_gromacs.sh --pre pressure gromacs calc_pressure_gromacs.sh pressure lammps calc_pressure_lammps.sh rdf gromacs calc_rdf_generic.sh imc_stat gromacs imc_stat_generic.sh density gromacs calc_density_generic.sh convert_potential gromacs potential_to_gromacs.sh convert_potentials gromacs potentials_to_generic.sh convert_potential xvg table_to_xvg.pl functions gromacs functions_gromacs.sh initstep espresso initialize_step_genericsim.sh run espresso run_genericsim.sh clean espresso clean_generic.sh rdf espresso calc_rdf_generic.sh imc_stat espresso imc_stat_generic.sh density espresso calc_density_generic.sh convert_potential espresso potential_to_generic.sh convert_potentials espresso potentials_to_generic.sh functions espresso functions_genericsim.sh convert_potential lammps potential_to_lammps.sh convert_potentials lammps potentials_to_generic.sh initstep lammps initialize_step_genericsim.sh run lammps run_genericsim.sh clean lammps clean_generic.sh rdf lammps calc_rdf_generic.sh imc_stat lammps imc_stat_generic.sh density lammps calc_density_generic.sh functions lammps functions_genericsim.sh convert_potential espressopp potential_to_generic.sh convert_potentials espressopp potentials_to_generic.sh initstep espressopp initialize_step_genericsim.sh run espressopp run_genericsim.sh clean espressopp clean_generic.sh rdf espressopp calc_rdf_generic.sh imc_stat espressopp imc_stat_generic.sh density espressopp calc_density_generic.sh functions espressopp functions_genericsim.sh initstep dlpoly initialize_step_genericsim.sh run dlpoly run_genericsim.sh clean dlpoly clean_generic.sh rdf dlpoly calc_rdf_generic.sh imc_stat dlpoly imc_stat_generic.sh density dlpoly calc_density_generic.sh functions dlpoly functions_dlpoly.sh convert_potential dlpoly potential_to_dlpoly.sh convert_potentials dlpoly potentials_to_dlpoly.sh convert_potential hoomd-blue potential_to_generic.sh convert_potentials hoomd-blue potentials_to_generic.sh initstep hoomd-blue initialize_step_genericsim.sh run hoomd-blue run_genericsim.sh clean hoomd-blue clean_generic.sh rdf hoomd-blue calc_rdf_generic.sh imc_stat hoomd-blue imc_stat_generic.sh density hoomd-blue calc_density_generic.sh functions hoomd-blue functions_genericsim.sh ------------------------ Prepare (dir step_000) ------------------------ Running critical command 'pushd /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb' ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000 cp_from_main_dir: 'grompp.mdp topol.top table.xvg index.ndx table_b0.xvg table_b1.xvg table_a0.xvg table_a1.xvg' Running critical command 'cp grompp.mdp topol.top table.xvg index.ndx table_b0.xvg table_b1.xvg table_a0.xvg table_a1.xvg /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000' Running critical command 'popd' ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000 Running subscript 'prepare_generic.sh' (from tags prepare ibi) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse csg_get_property: No value for 'cg.bonded.name' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.bonded.name' csg_get_property: No value for 'cg.bonded.min' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.bonded.min' For all bonded csg_get_property: No value for 'cg.bonded.name' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.bonded.name' For all non-bonded for_all: run 'do_external prepare_single ibi' for interaction named 'A-A' Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Using initial guess from dist A-A.dist.tgt for A-A Running subscript 'resample_target.sh A-A.dist.tgt A-A.dist.tgt' (from tags resample target) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running critical command 'mktemp A-A.dist.tgt_smooth.XXXXX' Running critical command 'csg_resample --in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/A-A.dist.tgt --out A-A.dist.tgt_smooth.bh1Iu --grid 0.00:0.01:1.50 --comment Created on Wed Aug 5 18:11:56 IST 2020 by pragati@HP38 called from resample_target.sh, version 1.7-dev gitid: a446925 settings file: '/home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml' working directory: /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000' Running critical command 'mktemp A-A.dist.tgt_extrapolated.XXXXX' Running critical command 'mktemp A-A.dist.tgt_extrapolated_left.XXXXX' Running subscript 'table_extrapolate.pl --function linear --avgpoints 1 --region left A-A.dist.tgt_smooth.bh1Iu A-A.dist.tgt_extrapolated_left.yuCon' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using linear with gradient 0 Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-A.dist.tgt_extrapolated_left.yuCon A-A.dist.tgt_extrapolated.HG99v' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the right using constant with gradient 0 Running subscript 'dist_adjust.pl A-A.dist.tgt_extrapolated.HG99v A-A.dist.tgt' (from tags dist adjust) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running critical command 'mktemp A-A.pot.new.raw.XXX' csg_get_property: No value for 'cg.inverse.dist_min' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.dist_min' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: 1e-10 Running subscript 'dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435 --min 1e-10 A-A.dist.tgt A-A.pot.new.raw.75T' (from tags dist invert) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running critical command 'mktemp A-A.pot.new.smooth.XXX' Running critical command 'csg_resample --in A-A.pot.new.raw.75T --out A-A.pot.new.smooth.B5I --grid 0.00:0.01:1.50 --comment Created on Wed Aug 5 18:11:56 IST 2020 by pragati@HP38 called from prepare_generic_single.sh, version 1.7-dev gitid: a446925 settings file: '/home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml' working directory: /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000' Running critical command 'mktemp A-A.pot.new.extrapolate.XXX' Running subscript 'potential_extrapolate.sh --type non-bonded A-A.pot.new.smooth.B5I A-A.pot.new.extrapolate.gTQ' (from tags potential extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Extrapolate A-A.pot.new.smooth.B5I to A-A.pot.new.extrapolate.gTQ Running critical command 'mktemp A-A.pot.new.smooth.B5I.onlyleft.XXXXX' Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left A-A.pot.new.smooth.B5I A-A.pot.new.smooth.B5I.onlyleft.Jb9WY' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using exponential with gradient -475.641767666666 Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-A.pot.new.smooth.B5I.onlyleft.Jb9WY A-A.pot.new.extrapolate.gTQ' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the right using constant with gradient 0 Running critical command 'mktemp A-A.pot.new.shifted.XXX' Running subscript 'potential_shift.pl --type non-bonded A-A.pot.new.extrapolate.gTQ A-A.pot.new.shifted.ujN' (from tags potential shift) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running subscript 'table_change_flag.sh A-A.pot.new.shifted.ujN A-A.pot.new' (from tags table change_flag) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running critical command 'sed -e s/o$/i/ A-A.pot.new.shifted.ujN' for_all: run 'do_external prepare_single ibi' for interaction named 'A-B' Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Using initial guess from dist A-B.dist.tgt for A-B Running subscript 'resample_target.sh A-B.dist.tgt A-B.dist.tgt' (from tags resample target) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running critical command 'mktemp A-B.dist.tgt_smooth.XXXXX' Running critical command 'csg_resample --in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/A-B.dist.tgt --out A-B.dist.tgt_smooth.50L1M --grid 0.00:0.01:1.50 --comment Created on Wed Aug 5 18:11:57 IST 2020 by pragati@HP38 called from resample_target.sh, version 1.7-dev gitid: a446925 settings file: '/home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml' working directory: /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000' Running critical command 'mktemp A-B.dist.tgt_extrapolated.XXXXX' Running critical command 'mktemp A-B.dist.tgt_extrapolated_left.XXXXX' Running subscript 'table_extrapolate.pl --function linear --avgpoints 1 --region left A-B.dist.tgt_smooth.50L1M A-B.dist.tgt_extrapolated_left.p3yBT' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using linear with gradient 0 Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-B.dist.tgt_extrapolated_left.p3yBT A-B.dist.tgt_extrapolated.NidQ2' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the right using constant with gradient 0 Running subscript 'dist_adjust.pl A-B.dist.tgt_extrapolated.NidQ2 A-B.dist.tgt' (from tags dist adjust) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running critical command 'mktemp A-B.pot.new.raw.XXX' csg_get_property: No value for 'cg.inverse.dist_min' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.dist_min' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: 1e-10 Running subscript 'dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435 --min 1e-10 A-B.dist.tgt A-B.pot.new.raw.YlL' (from tags dist invert) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running critical command 'mktemp A-B.pot.new.smooth.XXX' Running critical command 'csg_resample --in A-B.pot.new.raw.YlL --out A-B.pot.new.smooth.u8E --grid 0.00:0.01:1.50 --comment Created on Wed Aug 5 18:11:57 IST 2020 by pragati@HP38 called from prepare_generic_single.sh, version 1.7-dev gitid: a446925 settings file: '/home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml' working directory: /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000' Running critical command 'mktemp A-B.pot.new.extrapolate.XXX' Running subscript 'potential_extrapolate.sh --type non-bonded A-B.pot.new.smooth.u8E A-B.pot.new.extrapolate.2Rx' (from tags potential extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Extrapolate A-B.pot.new.smooth.u8E to A-B.pot.new.extrapolate.2Rx Running critical command 'mktemp A-B.pot.new.smooth.u8E.onlyleft.XXXXX' Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left A-B.pot.new.smooth.u8E A-B.pot.new.smooth.u8E.onlyleft.RR60A' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using exponential with gradient -373.388413333334 Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-B.pot.new.smooth.u8E.onlyleft.RR60A A-B.pot.new.extrapolate.2Rx' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the right using constant with gradient 0 Running critical command 'mktemp A-B.pot.new.shifted.XXX' Running subscript 'potential_shift.pl --type non-bonded A-B.pot.new.extrapolate.2Rx A-B.pot.new.shifted.UMP' (from tags potential shift) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running subscript 'table_change_flag.sh A-B.pot.new.shifted.UMP A-B.pot.new' (from tags table change_flag) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running critical command 'sed -e s/o$/i/ A-B.pot.new.shifted.UMP' for_all: run 'do_external prepare_single ibi' for interaction named 'B-B' Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Using initial guess from dist B-B.dist.tgt for B-B Running subscript 'resample_target.sh B-B.dist.tgt B-B.dist.tgt' (from tags resample target) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running critical command 'mktemp B-B.dist.tgt_smooth.XXXXX' Running critical command 'csg_resample --in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/B-B.dist.tgt --out B-B.dist.tgt_smooth.3Y92D --grid 0.00:0.01:1.50 --comment Created on Wed Aug 5 18:11:58 IST 2020 by pragati@HP38 called from resample_target.sh, version 1.7-dev gitid: a446925 settings file: '/home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml' working directory: /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000' Running critical command 'mktemp B-B.dist.tgt_extrapolated.XXXXX' Running critical command 'mktemp B-B.dist.tgt_extrapolated_left.XXXXX' Running subscript 'table_extrapolate.pl --function linear --avgpoints 1 --region left B-B.dist.tgt_smooth.3Y92D B-B.dist.tgt_extrapolated_left.yehe9' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using linear with gradient 0 Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right B-B.dist.tgt_extrapolated_left.yehe9 B-B.dist.tgt_extrapolated.tGOUh' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the right using constant with gradient 0 Running subscript 'dist_adjust.pl B-B.dist.tgt_extrapolated.tGOUh B-B.dist.tgt' (from tags dist adjust) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running critical command 'mktemp B-B.pot.new.raw.XXX' csg_get_property: No value for 'cg.inverse.dist_min' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.dist_min' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: 1e-10 Running subscript 'dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435 --min 1e-10 B-B.dist.tgt B-B.pot.new.raw.Ato' (from tags dist invert) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running critical command 'mktemp B-B.pot.new.smooth.XXX' Running critical command 'csg_resample --in B-B.pot.new.raw.Ato --out B-B.pot.new.smooth.wSf --grid 0.00:0.01:1.50 --comment Created on Wed Aug 5 18:11:58 IST 2020 by pragati@HP38 called from prepare_generic_single.sh, version 1.7-dev gitid: a446925 settings file: '/home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml' working directory: /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000' Running critical command 'mktemp B-B.pot.new.extrapolate.XXX' Running subscript 'potential_extrapolate.sh --type non-bonded B-B.pot.new.smooth.wSf B-B.pot.new.extrapolate.jAs' (from tags potential extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Extrapolate B-B.pot.new.smooth.wSf to B-B.pot.new.extrapolate.jAs Running critical command 'mktemp B-B.pot.new.smooth.wSf.onlyleft.XXXXX' Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left B-B.pot.new.smooth.wSf B-B.pot.new.smooth.wSf.onlyleft.6fcop' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using exponential with gradient -456.062706 Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right B-B.pot.new.smooth.wSf.onlyleft.6fcop B-B.pot.new.extrapolate.jAs' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the right using constant with gradient 0 Running critical command 'mktemp B-B.pot.new.shifted.XXX' Running subscript 'potential_shift.pl --type non-bonded B-B.pot.new.extrapolate.jAs B-B.pot.new.shifted.3QD' (from tags potential shift) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running subscript 'table_change_flag.sh B-B.pot.new.shifted.3QD B-B.pot.new' (from tags table change_flag) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running critical command 'sed -e s/o$/i/ B-B.pot.new.shifted.3QD' csg_get_property: No value for 'cg.bonded.name' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.bonded.name' csg_get_property: No value for 'cg.bonded.min' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.bonded.min' For all dihedral csg_get_property: No value for 'cg.bonded.name' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.bonded.name' step 0 done ------------------------------- Doing iteration 1 (dir step_001) ------------------------------- Step 1 started at Wed Aug 5 18:11:59 IST 2020 Running critical command 'pushd /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb' ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 cp_from_main_dir: 'grompp.mdp topol.top table.xvg index.ndx table_b0.xvg table_b1.xvg table_a0.xvg table_a1.xvg' Running critical command 'cp grompp.mdp topol.top table.xvg index.ndx table_b0.xvg table_b1.xvg table_a0.xvg table_a1.xvg /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001' Running critical command 'popd' ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 Running subscript 'initialize_step_generic.sh' (from tags initstep ibi) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse csg_get_property: No value for 'cg.bonded.name' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.bonded.name' csg_get_property: No value for 'cg.bonded.min' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.bonded.min' For all non-bonded for_all: run 'cp_from_last_step --rename $(csg_get_interaction_property name).pot.new $(csg_get_interaction_property name).pot.cur' for interaction named 'A-A' cp_from_last_step: 'A-A.pot.new' to 'A-A.pot.cur' Running critical command 'pushd /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000' ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000 ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 Running critical command 'cp A-A.pot.new /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001/A-A.pot.cur' Running critical command 'popd' ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 for_all: run 'cp_from_last_step --rename $(csg_get_interaction_property name).pot.new $(csg_get_interaction_property name).pot.cur' for interaction named 'A-B' cp_from_last_step: 'A-B.pot.new' to 'A-B.pot.cur' Running critical command 'pushd /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000' ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000 ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 Running critical command 'cp A-B.pot.new /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001/A-B.pot.cur' Running critical command 'popd' ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 for_all: run 'cp_from_last_step --rename $(csg_get_interaction_property name).pot.new $(csg_get_interaction_property name).pot.cur' for interaction named 'B-B' cp_from_last_step: 'B-B.pot.new' to 'B-B.pot.cur' Running critical command 'pushd /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000' ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000 ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 Running critical command 'cp B-B.pot.new /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001/B-B.pot.cur' Running critical command 'popd' ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 For all bonded csg_get_property: No value for 'cg.bonded.name' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.bonded.name' Running subscript 'initialize_step_genericsim.sh' (from tags initstep gromacs) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse csg_get_property: No value for 'cg.inverse.initial_configuration' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.initial_configuration' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: maindir csg_get_property: No value for 'cg.inverse.gromacs.conf' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.conf' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: conf.gro Using intial configuration from maindir Running critical command 'pushd /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb' ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 cp_from_main_dir: 'conf.gro' Running critical command 'cp conf.gro /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001' Running critical command 'popd' ~/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 Running subscript 'potentials_to_generic.sh' (from tags convert_potentials gromacs) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse csg_get_property: No value for 'cg.bonded.name' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.bonded.name' csg_get_property: No value for 'cg.bonded.min' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.bonded.min' For all non-bonded for_all: run 'do_external convert_potential gromacs $(csg_get_interaction_property name).pot.cur $(csg_get_interaction_property inverse.gromacs.table)' for interaction named 'A-A' Running subscript 'potential_to_gromacs.sh A-A.pot.cur table_A_A.xvg' (from tags convert_potential gromacs) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Convert A-A.pot.cur to table_A_A.xvg csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp Found setting file 'grompp.mdp' now trying to check options in there csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp Running critical command 'mktemp A-A.pot.smooth.XXXXX' Running critical command 'csg_resample --in A-A.pot.cur --out A-A.pot.smooth.xA7qz --grid 0:0.01:3.0' Running critical command 'mktemp A-A.pot.extrapol.XXXXX' Running subscript 'potential_extrapolate.sh --type non-bonded A-A.pot.smooth.xA7qz A-A.pot.extrapol.BQZ20' (from tags potential extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Extrapolate A-A.pot.smooth.xA7qz to A-A.pot.extrapol.BQZ20 Running critical command 'mktemp A-A.pot.smooth.xA7qz.onlyleft.XXXXX' Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left A-A.pot.smooth.xA7qz A-A.pot.smooth.xA7qz.onlyleft.kpB87' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using exponential with gradient -48111.1377 Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-A.pot.smooth.xA7qz.onlyleft.kpB87 A-A.pot.extrapol.BQZ20' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the right using constant with gradient 0 Running critical command 'mktemp A-A.pot.interpol.XXXXX' Running critical command 'csg_resample --in A-A.pot.extrapol.BQZ20 --out A-A.pot.interpol.LgTiM --grid 0:0.002:3.0 --comment Created on Wed Aug 5 18:12:01 IST 2020 by pragati@HP38 called from potential_to_gromacs.sh, version 1.7-dev gitid: a446925 settings file: '/home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml' working directory: /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 Comments from /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001/A-A.pot.cur:\nCreated on Wed Aug 5 18:11:56 IST 2020 by pragati@HP38 called from prepare_generic_single.sh, version 1.7-dev gitid: a446925 settings file: '/home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml' working directory: /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000' Running critical command 'mktemp A-A.pot.shift.XXXXX' Running subscript 'potential_shift.pl --type non-bonded A-A.pot.interpol.LgTiM A-A.pot.shift.doiJ1' (from tags potential shift) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running subscript 'table_to_xvg.pl --max 1000000 --type non-bonded A-A.pot.shift.doiJ1 table_A_A.xvg' (from tags convert_potential xvg) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse for_all: run 'do_external convert_potential gromacs $(csg_get_interaction_property name).pot.cur $(csg_get_interaction_property inverse.gromacs.table)' for interaction named 'A-B' Running subscript 'potential_to_gromacs.sh A-B.pot.cur table_A_B.xvg' (from tags convert_potential gromacs) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Convert A-B.pot.cur to table_A_B.xvg csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp Found setting file 'grompp.mdp' now trying to check options in there csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp Running critical command 'mktemp A-B.pot.smooth.XXXXX' Running critical command 'csg_resample --in A-B.pot.cur --out A-B.pot.smooth.XILZb --grid 0:0.01:3.0' Running critical command 'mktemp A-B.pot.extrapol.XXXXX' Running subscript 'potential_extrapolate.sh --type non-bonded A-B.pot.smooth.XILZb A-B.pot.extrapol.K5tec' (from tags potential extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Extrapolate A-B.pot.smooth.XILZb to A-B.pot.extrapol.K5tec Running critical command 'mktemp A-B.pot.smooth.XILZb.onlyleft.XXXXX' Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left A-B.pot.smooth.XILZb A-B.pot.smooth.XILZb.onlyleft.qpqr2' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using exponential with gradient -44593.2568333333 Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right A-B.pot.smooth.XILZb.onlyleft.qpqr2 A-B.pot.extrapol.K5tec' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the right using constant with gradient 0 Running critical command 'mktemp A-B.pot.interpol.XXXXX' Running critical command 'csg_resample --in A-B.pot.extrapol.K5tec --out A-B.pot.interpol.8lNTc --grid 0:0.002:3.0 --comment Created on Wed Aug 5 18:12:02 IST 2020 by pragati@HP38 called from potential_to_gromacs.sh, version 1.7-dev gitid: a446925 settings file: '/home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml' working directory: /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 Comments from /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001/A-B.pot.cur:\nCreated on Wed Aug 5 18:11:57 IST 2020 by pragati@HP38 called from prepare_generic_single.sh, version 1.7-dev gitid: a446925 settings file: '/home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml' working directory: /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000' Running critical command 'mktemp A-B.pot.shift.XXXXX' Running subscript 'potential_shift.pl --type non-bonded A-B.pot.interpol.8lNTc A-B.pot.shift.XpvHB' (from tags potential shift) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running subscript 'table_to_xvg.pl --max 1000000 --type non-bonded A-B.pot.shift.XpvHB table_A_B.xvg' (from tags convert_potential xvg) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse for_all: run 'do_external convert_potential gromacs $(csg_get_interaction_property name).pot.cur $(csg_get_interaction_property inverse.gromacs.table)' for interaction named 'B-B' Running subscript 'potential_to_gromacs.sh B-B.pot.cur table_B_B.xvg' (from tags convert_potential gromacs) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Convert B-B.pot.cur to table_B_B.xvg csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp Found setting file 'grompp.mdp' now trying to check options in there csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp Running critical command 'mktemp B-B.pot.smooth.XXXXX' Running critical command 'csg_resample --in B-B.pot.cur --out B-B.pot.smooth.uCh6x --grid 0:0.01:3.0' Running critical command 'mktemp B-B.pot.extrapol.XXXXX' Running subscript 'potential_extrapolate.sh --type non-bonded B-B.pot.smooth.uCh6x B-B.pot.extrapol.3l7lR' (from tags potential extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Extrapolate B-B.pot.smooth.uCh6x to B-B.pot.extrapol.3l7lR Running critical command 'mktemp B-B.pot.smooth.uCh6x.onlyleft.XXXXX' Running subscript 'table_extrapolate.pl --function exponential --avgpoints 3 --region left B-B.pot.smooth.uCh6x B-B.pot.smooth.uCh6x.onlyleft.ozDWQ' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using exponential with gradient -52280.7858666667 Running subscript 'table_extrapolate.pl --function constant --avgpoints 1 --region right B-B.pot.smooth.uCh6x.onlyleft.ozDWQ B-B.pot.extrapol.3l7lR' (from tags table extrapolate) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the right using constant with gradient 0 Running critical command 'mktemp B-B.pot.interpol.XXXXX' Running critical command 'csg_resample --in B-B.pot.extrapol.3l7lR --out B-B.pot.interpol.gqR65 --grid 0:0.002:3.0 --comment Created on Wed Aug 5 18:12:02 IST 2020 by pragati@HP38 called from potential_to_gromacs.sh, version 1.7-dev gitid: a446925 settings file: '/home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml' working directory: /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 Comments from /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001/B-B.pot.cur:\nCreated on Wed Aug 5 18:11:58 IST 2020 by pragati@HP38 called from prepare_generic_single.sh, version 1.7-dev gitid: a446925 settings file: '/home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml' working directory: /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_000' Running critical command 'mktemp B-B.pot.shift.XXXXX' Running subscript 'potential_shift.pl --type non-bonded B-B.pot.interpol.gqR65 B-B.pot.shift.q6kn7' (from tags potential shift) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse Running subscript 'table_to_xvg.pl --max 1000000 --type non-bonded B-B.pot.shift.q6kn7 table_B_B.xvg' (from tags convert_potential xvg) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse For all bonded csg_get_property: No value for 'cg.bonded.name' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.bonded.name' Simulation with gromacs Running subscript 'run_gromacs.sh' (from tags run gromacs) dir /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse csg_get_property: No value for 'cg.inverse.gromacs.topol' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.topol' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: topol.tpr csg_get_property: No value for 'cg.inverse.gromacs.mdrun.opts' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.mdrun.opts' csg_get_property: No value for 'cg.inverse.gromacs.mdrun.multidir' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.mdrun.multidir' csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp csg_get_property: No value for 'cg.inverse.gromacs.conf' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.conf' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: conf.gro csg_get_property: No value for 'cg.inverse.gromacs.conf_out' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.conf_out' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: confout.gro csg_get_property: No value for 'cg.inverse.gromacs.index' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.index' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: index.ndx csg_get_property: No value for 'cg.inverse.gromacs.topol_in' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.topol_in' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: topol.top csg_get_property: No value for 'cg.inverse.gromacs.grompp.opts' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.grompp.opts' csg_get_property: No value for 'cg.inverse.gromacs.traj' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.traj' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: traj.xtc csg_get_property: No value for 'cg.inverse.gromacs.temp_check' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.temp_check' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: yes csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp csg_get_property: No value for 'cg.inverse.gromacs.pre_simulation' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.pre_simulation' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: no csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: value for 'cg.inverse.gromacs.mdp' from /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml: grompp.mdp Automatically added 'cutoff-scheme = Group' to grompp.mdp, tabulated interactions only work with Group cutoff-scheme! csg_get_property: No value for 'cg.inverse.gromacs.log' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.log' Running critical command 'gmx_tmpi grompp -n index.ndx -f grompp.mdp -p topol.top -o topol.tpr -c conf.gro' :-) GROMACS - gmx grompp, 2019 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2019 Executable: /apps/GROMACS/gromacs-2019.0_tmpi/bin/gmx_tmpi Data prefix: /apps/GROMACS/gromacs-2019.0_tmpi Working dir: /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 Command line: gmx_tmpi grompp -n index.ndx -f grompp.mdp -p topol.top -o topol.tpr -c conf.gro NOTE 1 [file grompp.mdp]: The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future release when all interaction forms are supported for the verlet scheme. The verlet scheme already scales better, and it is compatible with GPUs and other accelerators. NOTE 2 [file grompp.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 3 [file grompp.mdp]: You have selected user tables with dispersion correction, the dispersion will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction between rvdw_switch and rvdw will not be double counted). Make sure that you really want dispersion correction to -C6/r^6. NOTE 4 [file grompp.mdp]: You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = PME-Switch or Reaction-Field-zero Generated 3 of the 3 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'CGBUT' Setting gen_seed to 1547232539 Velocities were taken from a Maxwell distribution at 300 K Number of degrees of freedom in T-Coupling group System is 5997.00 There were 4 notes GROMACS reminds you: "Years of calculations and the stress, My science is waiting, nearly complete" (Midlake) This run will generate roughly 14 Mb of data run_gromacs.sh: No walltime defined, so no time limitation given to gmx_tmpi mdrun Automatically added '-tableb table_a0.xvg table_a1.xvg table_b0.xvg table_b1.xvg to mdrun options (add -tableb option to cg.inverse.gromacs.mdrun.opts yourself if this is wrong) csg_get_property: No value for 'cg.inverse.gromacs.log' found in /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/settings.xml, trying /apps/VOTCA/votca-wdgromacs/share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.log' Running critical command 'gmx_tmpi mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -tableb table_a0.xvg table_a1.xvg table_b0.xvg table_b1.xvg' :-) GROMACS - gmx mdrun, 2019 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2019 Executable: /apps/GROMACS/gromacs-2019.0_tmpi/bin/gmx_tmpi Data prefix: /apps/GROMACS/gromacs-2019.0_tmpi Working dir: /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/step_001 Command line: gmx_tmpi mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -tableb table_a0.xvg table_a1.xvg table_b0.xvg table_b1.xvg Reading file topol.tpr, VERSION 2019 (single precision) NOTE: GPU(s) found, but the current simulation can not use GPUs To use a GPU, set the mdp option: cutoff-scheme = Verlet Multiple energy groups is not implemented for GPUs, falling back to the CPU. For better performance, run on the GPU without energy groups and then do gmx mdrun -rerun option on the trajectory with an energy group .tpr file. NOTE: Parallelization is limited by the small number of atoms, only starting 12 thread-MPI ranks. You can use the -nt and/or -ntmpi option to optimize the number of threads. Using 12 MPI threads NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be removed in a future release when 'verlet' supports all interaction forms. starting mdrun 'other' 100000 steps, 200.0 ps. /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse/run_gromacs.sh: line 1: 16396 Segmentation fault (core dumped) "$@" Callstack: /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse/inverse.sh - linenumber 246 do_external - linenumber 176 in /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse/functions_common.sh /apps/VOTCA/votca-wdgromacs/share/votca/scripts/inverse/run_gromacs.sh - linenumber 184 critical - linenumber 4 (see 'csg_call --cat function critical') die - linenumber 2 (see 'csg_call --cat function die') ##################################################################################################################################################### # # # ERROR: # # critical: 'gmx_tmpi mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -tableb table_a0.xvg table_a1.xvg table_b0.xvg table_b1.xvg' failed # # For details see the logfile /home/pragati/Data/CG-IBI/coarsegrained/atomistic/melt/1ns/NVT/csg_boltz_nonb/inverse.log # # # ##################################################################################################################################################### die: (called from 15894) CSG_MASTER_PID is 12224 die: pids to kill: 12224 15894