Hi all, I am trying to use IBI to refine one of the bonded potentials in my CG system. The initial guess and step_001 gromacs simulation run without issue, but it fails to update the potential at this step. The detailed error output from inverse.log is pasted below. It seems to me that the issue isn't with the potential_shift.pl step, which (I think) just fails because SNa-SC2.dpot.pure_ibi has no non-zero values in it; I think the problem arises during the "update_ibi_pot" step when dU is calculated. I noticed that the current rdf is quite far from the target distribution and wonder if this could be causing some problems? I've attached the two distributions, the current potential and pure_ibi files, and the full log file. Please let me know if there is any other information I can provide that will be of help troubleshooting this problem.
------------------------------------from
inverse.log---------------------------------------------------------------
Running critical command 'mktemp SNa-SC2.dist.tgt_extrapolated.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 1
--region leftright SNa-SC2.dist.tgt_smooth.PP6mM
SNa-SC2.dist.tgt_extrapolated.w36Sf' (from tags table extrapolate) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 0
table_extrapolate.pl: extrapolating the right using linear with gradient 0
Running subscript 'dist_adjust.pl SNa-SC2.dist.tgt_extrapolated.w36Sf
SNa-SC2.dist.tgt' (from tags dist adjust) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
Running subscript 'update_ibi_pot.pl SNa-SC2.dist.tgt SNa-SC2.dist.new
SNa-SC2.pot.cur SNa-SC2.dpot.pure_ibi 2.49435' (from tags update ibi_pot)
dir /home/arice3/Programs/votca/share/votca/scripts/inverse
Running subscript 'potential_shift.pl --type bond SNa-SC2.dpot.pure_ibi
SNa-SC2.dpot.new' (from tags potential shift) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
No valid value found in SNa-SC2.dpot.pure_ibi at
/home/arice3/Programs/votca/share/votca/scripts/inverse/potential_shift.pl
line 87.
Callstack:
/home/arice3/Programs/votca/share/votca/scripts/inverse/inverse.sh -
linenumber 264
do_external - linenumber 176 in
/home/arice3/Programs/votca/share/votca/scripts/inverse/functions_common.sh
/home/arice3/Programs/votca/share/votca/scripts/inverse/update_ibi.sh -
linenumber 32
for_all - linenumber 22 (see 'csg_call --cat function for_all')
do_external - linenumber 19 (see 'csg_call --cat
function do_external')
/home/arice3/Programs/votca/share/votca/scripts/inverse/update_ibi_single.sh
- linenumber 42
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/arice3/Programs/votca/share/votca/scripts/inverse/potential_shift.pl
--type bond SNa-SC2.dpot.pure_ibi SNa-SC2.dpot.new #
# (from tags potential shift)
failed
#
# For details see the logfile
/local/VOTCA/IBI_test/inverse.log
#
#
#
#################################################################################################################################
die: (called from 16487) CSG_MASTER_PID is 12694
die: pids to kill: 12694 15891 16472 16487
-----------------------------------------------------------------------------------------------------------------------------------------------
Thank you for the help,
- Amy
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SNa-SC2.dpot.pure_ibi
Description: Binary data
SNa-SC2.dist.tgt
Description: Binary data
SNa-SC2.dist.new
Description: Binary data
SNa-SC2.pot.cur
Description: Binary data
For a more verbose log see: inverse.log
csg_get_property: No value for 'cg.inverse.mpi.tasks' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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 /local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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 /local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.imc.numpy.bin'
Sim started Wed Mar 14 14:36:17 CDT 2018
We are doing Method: ibi
csg_get_property: No value for 'cg.inverse.scriptpath' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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 /home/arice3/Programs/votca/share/votca/scripts/inverse
#From: /home/arice3/Programs/votca/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
prepare ibm prepare_ibm.sh
update ibm update_ibm.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
dpot crop dpot_crop.pl
update ibi update_ibi.sh
update ibi_single update_ibi_single.sh
update ibi_pot update_ibi_pot.pl
update imc update_imc.sh
imcsolver matlab solve_matlab.sh
solve matlab linsolve.m
imcsolver octave solve_octave.sh
solve octave linsolve.octave
imcsolver numpy solve_numpy.sh
solve numpy linsolve.py
imc purify imc_purify.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 getsubset table_getsubset.py
table smooth_borders table_smooth_borders.py
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
configuration compare configuration_compare.py
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 /local/VOTCA/IBI_test'
/local/VOTCA/IBI_test /local/VOTCA/IBI_test/step_000
cp_from_main_dir: 'grompp.mdp topol.top table_b1_b1.xvg index.ndx'
Running critical command 'cp grompp.mdp topol.top table_b1_b1.xvg index.ndx
/local/VOTCA/IBI_test/step_000'
Running critical command 'popd'
/local/VOTCA/IBI_test/step_000
Running subscript 'prepare_generic.sh' (from tags prepare ibi) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
csg_get_property: No value for 'cg.non-bonded.name' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.name'
csg_get_property: No value for 'cg.non-bonded.min' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.min'
For all bonded
for_all: run 'do_external prepare_single ibi' for interaction named 'SNa-SC2'
Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi)
dir /home/arice3/Programs/votca/share/votca/scripts/inverse
Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p'
Using initial guess from dist SNa-SC2.tgt for SNa-SC2
Running subscript 'resample_target.sh SNa-SC2.tgt SNa-SC2.dist.tgt' (from tags
resample target) dir /home/arice3/Programs/votca/share/votca/scripts/inverse
Running critical command 'mktemp SNa-SC2.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in /local/VOTCA/IBI_test/SNa-SC2.tgt
--out SNa-SC2.dist.tgt_smooth.YkTCd --grid 0.15:0.002:0.45 --comment Created on
Wed Mar 14 14:36:18 CDT 2018 by arice3@mead
called from resample_target.sh, version 1.5-dev gitid: 65d1f9c
settings file: '/local/VOTCA/IBI_test/settings.xml'
working directory: /local/VOTCA/IBI_test/step_000'
Running critical command 'mktemp SNa-SC2.dist.tgt_extrapolated.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 1
--region leftright SNa-SC2.dist.tgt_smooth.YkTCd
SNa-SC2.dist.tgt_extrapolated.ZAQnz' (from tags table extrapolate) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 0
table_extrapolate.pl: extrapolating the right using linear with gradient 0
Running subscript 'dist_adjust.pl SNa-SC2.dist.tgt_extrapolated.ZAQnz
SNa-SC2.dist.tgt' (from tags dist adjust) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
Running critical command 'mktemp SNa-SC2.pot.new.raw.XXX'
csg_get_property: No value for 'cg.inverse.dist_min' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.dist_min' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: 1e-10
Running subscript 'dist_boltzmann_invert.pl --type bond --kbT 2.49435 --min
1e-10 SNa-SC2.dist.tgt SNa-SC2.pot.new.raw.TZZ' (from tags dist invert) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
Running critical command 'mktemp SNa-SC2.pot.new.smooth.XXX'
Running critical command 'csg_resample --in SNa-SC2.pot.new.raw.TZZ --out
SNa-SC2.pot.new.smooth.r5b --grid 0.15:0.002:0.45 --comment Created on Wed Mar
14 14:36:17 CDT 2018 by arice3@mead
called from prepare_generic_single.sh, version 1.5-dev gitid: 65d1f9c
settings file: '/local/VOTCA/IBI_test/settings.xml'
working directory: /local/VOTCA/IBI_test/step_000'
Running critical command 'mktemp SNa-SC2.pot.new.extrapolate.XXX'
Running subscript 'potential_extrapolate.sh --type bond
SNa-SC2.pot.new.smooth.r5b SNa-SC2.pot.new.extrapolate.EnH' (from tags
potential extrapolate) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
Extrapolate SNa-SC2.pot.new.smooth.r5b to SNa-SC2.pot.new.extrapolate.EnH
Running critical command 'mktemp SNa-SC2.pot.new.smooth.r5b.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 3
--region left SNa-SC2.pot.new.smooth.r5b
SNa-SC2.pot.new.smooth.r5b.onlyleft.BlPbT' (from tags table extrapolate) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient
-2088.813844
Running subscript 'table_extrapolate.pl --function linear --avgpoints 3
--region right SNa-SC2.pot.new.smooth.r5b.onlyleft.BlPbT
SNa-SC2.pot.new.extrapolate.EnH' (from tags table extrapolate) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using linear with gradient
2530.77997583333
Running critical command 'mktemp SNa-SC2.pot.new.shifted.XXX'
Running subscript 'potential_shift.pl --type bond
SNa-SC2.pot.new.extrapolate.EnH SNa-SC2.pot.new.shifted.Pp0' (from tags
potential shift) dir /home/arice3/Programs/votca/share/votca/scripts/inverse
Running subscript 'table_change_flag.sh SNa-SC2.pot.new.shifted.Pp0
SNa-SC2.pot.new' (from tags table change_flag) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
Running critical command 'sed -e s/o$/i/ SNa-SC2.pot.new.shifted.Pp0'
For all non-bonded
csg_get_property: No value for 'cg.non-bonded.name' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.name'
step 0 done
We are doing 1 of 500 iterations (0=inf).
-------------------------------
Doing iteration 1 (dir step_001)
-------------------------------
Step 1 started at Wed Mar 14 14:36:18 CDT 2018
Running critical command 'pushd /local/VOTCA/IBI_test'
/local/VOTCA/IBI_test /local/VOTCA/IBI_test/step_001
cp_from_main_dir: 'grompp.mdp topol.top table_b1_b1.xvg index.ndx'
Running critical command 'cp grompp.mdp topol.top table_b1_b1.xvg index.ndx
/local/VOTCA/IBI_test/step_001'
Running critical command 'popd'
/local/VOTCA/IBI_test/step_001
Running subscript 'initialize_step_generic.sh' (from tags initstep ibi) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
csg_get_property: No value for 'cg.non-bonded.name' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.name'
csg_get_property: No value for 'cg.non-bonded.min' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.min'
For all non-bonded
csg_get_property: No value for 'cg.non-bonded.name' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.name'
For all 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 'SNa-SC2'
cp_from_last_step: 'SNa-SC2.pot.new' to 'SNa-SC2.pot.cur'
Running critical command 'pushd /local/VOTCA/IBI_test/step_000'
/local/VOTCA/IBI_test/step_000 /local/VOTCA/IBI_test/step_001
Running critical command 'cp SNa-SC2.pot.new
/local/VOTCA/IBI_test/step_001/SNa-SC2.pot.cur'
Running critical command 'popd'
/local/VOTCA/IBI_test/step_001
Running subscript 'initialize_step_genericsim.sh' (from tags initstep gromacs)
dir /home/arice3/Programs/votca/share/votca/scripts/inverse
csg_get_property: No value for 'cg.inverse.initial_configuration' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.initial_configuration' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: maindir
csg_get_property: No value for 'cg.inverse.gromacs.conf' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.conf' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: conf.gro
Using intial configuration from maindir
Running critical command 'pushd /local/VOTCA/IBI_test'
/local/VOTCA/IBI_test /local/VOTCA/IBI_test/step_001
cp_from_main_dir: 'conf.gro'
Running critical command 'cp conf.gro /local/VOTCA/IBI_test/step_001'
Running critical command 'popd'
/local/VOTCA/IBI_test/step_001
Running subscript 'potentials_to_generic.sh' (from tags convert_potentials
gromacs) dir /home/arice3/Programs/votca/share/votca/scripts/inverse
csg_get_property: No value for 'cg.non-bonded.name' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.name'
csg_get_property: No value for 'cg.non-bonded.min' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.min'
For all non-bonded
csg_get_property: No value for 'cg.non-bonded.name' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.name'
For all 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 'SNa-SC2'
Running subscript 'potential_to_gromacs.sh SNa-SC2.pot.cur table_b1.xvg' (from
tags convert_potential gromacs) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
Convert SNa-SC2.pot.cur to table_b1.xvg
Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p'
Running critical command 'mktemp SNa-SC2.pot.smooth.XXXXX'
Running critical command 'csg_resample --in SNa-SC2.pot.cur --out
SNa-SC2.pot.smooth.1H85m --grid 0:0.002:4.5'
Running critical command 'mktemp SNa-SC2.pot.extrapol.XXXXX'
Running subscript 'potential_extrapolate.sh --type bond
SNa-SC2.pot.smooth.1H85m SNa-SC2.pot.extrapol.buOR5' (from tags potential
extrapolate) dir /home/arice3/Programs/votca/share/votca/scripts/inverse
Extrapolate SNa-SC2.pot.smooth.1H85m to SNa-SC2.pot.extrapol.buOR5
Running critical command 'mktemp SNa-SC2.pot.smooth.1H85m.onlyleft.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 3
--region left SNa-SC2.pot.smooth.1H85m SNa-SC2.pot.smooth.1H85m.onlyleft.sHmhr'
(from tags table extrapolate) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient
-2088.81385
Running subscript 'table_extrapolate.pl --function linear --avgpoints 3
--region right SNa-SC2.pot.smooth.1H85m.onlyleft.sHmhr
SNa-SC2.pot.extrapol.buOR5' (from tags table extrapolate) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the right using linear with gradient
2530.77996666667
Running critical command 'mktemp SNa-SC2.pot.interpol.XXXXX'
Running critical command 'csg_resample --in SNa-SC2.pot.extrapol.buOR5 --out
SNa-SC2.pot.interpol.SJy47 --grid 0:0.002:4.5 --comment Created on Wed Mar 14
14:36:19 CDT 2018 by arice3@mead
called from potential_to_gromacs.sh, version 1.5-dev gitid: 65d1f9c
settings file: '/local/VOTCA/IBI_test/settings.xml'
working directory: /local/VOTCA/IBI_test/step_001
Comments from /local/VOTCA/IBI_test/step_001/SNa-SC2.pot.cur:\nCreated on Wed
Mar 14 14:36:17 CDT 2018 by arice3@mead
called from prepare_generic_single.sh, version 1.5-dev gitid: 65d1f9c
settings file: '/local/VOTCA/IBI_test/settings.xml'
working directory: /local/VOTCA/IBI_test/step_000'
Running critical command 'mktemp SNa-SC2.pot.shift.XXXXX'
Running subscript 'potential_shift.pl --type bond SNa-SC2.pot.interpol.SJy47
SNa-SC2.pot.shift.Gq0t1' (from tags potential shift) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
Running subscript 'table_to_xvg.pl --max 1000000 --type bond
SNa-SC2.pot.shift.Gq0t1 table_b1.xvg' (from tags convert_potential xvg) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
Simulation with gromacs
Running subscript 'run_gromacs.sh' (from tags run gromacs) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
csg_get_property: No value for 'cg.inverse.gromacs.topol' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.topol' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: topol.tpr
csg_get_property: No value for 'cg.inverse.gromacs.mdrun.opts' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.mdp' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: grompp.mdp
csg_get_property: No value for 'cg.inverse.gromacs.conf' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.conf' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: conf.gro
csg_get_property: No value for 'cg.inverse.gromacs.conf_out' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.conf_out' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: confout.gro
csg_get_property: No value for 'cg.inverse.gromacs.index' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.index' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: index.ndx
csg_get_property: No value for 'cg.inverse.gromacs.topol_in' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.topol_in' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: topol.top
csg_get_property: No value for 'cg.inverse.gromacs.grompp.opts' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/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.grompp.bin' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.grompp.bin' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: /usr/bin/gmx
grompp
csg_get_property: No value for 'cg.inverse.gromacs.traj' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.traj' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: traj.xtc
csg_get_property: No value for 'cg.inverse.gromacs.temp_check' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.temp_check' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: yes
csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.mdp' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: grompp.mdp
csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.mdp' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: grompp.mdp
csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.mdp' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: grompp.mdp
csg_get_property: No value for 'cg.inverse.gromacs.mdrun.checkpoint' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.mdrun.checkpoint' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: state.cpt
csg_get_property: No value for 'cg.inverse.gromacs.pre_simulation' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.pre_simulation' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: no
csg_get_property: No value for 'cg.inverse.gromacs.mdp' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.mdp' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: grompp.mdp
csg_get_property: No value for 'cg.inverse.gromacs.log' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.gromacs.log'
Running critical command '/usr/bin/gmx grompp -n index.ndx -f grompp.mdp -p
topol.top -o topol.tpr -c conf.gro'
:-) GROMACS - gmx grompp, VERSION 5.1.2 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman 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) 2001-2015, 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 5.1.2
Executable: /usr/bin/gmx
Data prefix: /usr
Command line:
gmx grompp -n index.ndx -f grompp.mdp -p topol.top -o topol.tpr -c conf.gro
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
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.
Setting the LD random seed to 1611953469
Generated 0 of the 2485 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'LPSA'
NOTE 2 [file topol.top, line 277]:
System has non-zero total charge: -9.000000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Number of degrees of freedom in T-Coupling group LPS is 168.00
There were 2 notes
gcq#282: "'Nay. We are but men.' Rock!" (Tenacious D)
This run will generate roughly 8 Mb of data
csg_get_property: No value for 'cg.inverse.gromacs.mdrun.command' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.mdrun.command' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml:
/usr/local/gromacs/bin/gmx mdrun
run_gromacs.sh: No walltime defined, so no time limitation given to
/usr/local/gromacs/bin/gmx mdrun
Automatically added '-tableb table_b1_b1.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
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.gromacs.log'
Running critical command '/usr/local/gromacs/bin/gmx mdrun -s topol.tpr -c
confout.gro -o traj.trr -x traj.xtc -tableb table_b1_b1.xvg table_b1.xvg'
:-) GROMACS - gmx mdrun, 2016.5 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
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) 2001-2017, 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 2016.5
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /local/VOTCA/IBI_test/step_001
Command line:
gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -tableb
table_b1_b1.xvg table_b1.xvg
Running on 1 node with total 8 cores, 16 logical cores
Hardware detected:
CPU info:
Vendor: Intel
Brand: Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: AVX_256
Hardware topology: Full, with devices
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
NOTE: Parallelization is limited by the small number of atoms,
only starting 1 thread-MPI ranks.
You can use the -nt and/or -ntmpi option to optimize the number of
threads.
Using 1 MPI thread
NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
removed in a future release when 'verlet' supports all interaction forms.
NOTE: Thread affinity setting failed. This can cause performance degradation.
If you think your settings are correct, ask on the gmx-users list.
starting mdrun 'LPS_test'
1000000 steps, 20000.0 ps.
Writing final coordinates.
Core t (s) Wall t (s) (%)
Time: 24.489 24.489 100.0
(ns/day) (hour/ns)
Performance: 70562.846 0.000
GROMACS reminds you: "Royale With Cheese" (Pulp Fiction)
csg_get_property: No value for 'cg.inverse.gromacs.traj' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.traj' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: traj.xtc
csg_get_property: No value for 'cg.inverse.gromacs.conf_out' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.conf_out' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: confout.gro
Running subscript 'dummy.sh' (from tags pre_update ibi) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
Make update for ibi
Running subscript 'update_ibi.sh' (from tags update ibi) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
csg_get_property: No value for 'cg.non-bonded.name' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.name'
csg_get_property: No value for 'cg.non-bonded.min' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.min'
For all non-bonded
csg_get_property: No value for 'cg.non-bonded.name' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.name'
For all bonded
for_all: run 'do_external rdf gromacs' for interaction named 'SNa-SC2'
Running subscript 'calc_rdf_generic.sh' (from tags rdf gromacs) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
csg_get_property: No value for 'cg.inverse.gromacs.rdf.topol' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.gromacs.rdf.topol'
csg_get_property: No value for 'cg.inverse.gromacs.topol' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.topol' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: topol.tpr
csg_get_property: No value for 'cg.inverse.gromacs.rdf.traj' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.gromacs.rdf.traj'
csg_get_property: No value for 'cg.inverse.gromacs.traj' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.traj' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: traj.xtc
csg_get_property: No value for 'cg.inverse.gromacs.rdf.map' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.gromacs.rdf.map'
csg_get_property: No value for 'cg.inverse.gromacs.first_frame' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.first_frame' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: 0
csg_get_property: No value for 'cg.inverse.gromacs.rdf.with_errors' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.gromacs.rdf.with_errors' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: no
csg_get_property: No value for 'cg.inverse.simulation.tasks' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: value for 'cg.inverse.simulation.tasks' from
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml: auto
Calculating rdfs with csg_stat using 16 tasks
Running critical command 'csg_stat --nt 16 --options
/local/VOTCA/IBI_test/settings.xml --top topol.tpr --trj traj.xtc --begin 2500
--first-frame 0 --cg /local/VOTCA/IBI_test/LPS_cg.xml;'
begin to calculate distribution functions
# of bonded interactions: 1
# of non-bonded interactions: 0
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
I have 58 beads in 1 molecules
I have 58 beads in 1 molecules for the coarsegraining
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Note: file tpx version 103, software tpx version 110
written SNa-SC2.dist.new
csg_get_property: No value for 'cg.non-bonded.name' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.name'
csg_get_property: No value for 'cg.non-bonded.min' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.min'
For all non-bonded
csg_get_property: No value for 'cg.non-bonded.name' found in
/local/VOTCA/IBI_test/settings.xml, trying
/home/arice3/Programs/votca/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.non-bonded.name'
For all bonded
for_all: run 'do_external update ibi_single' for interaction named 'SNa-SC2'
Running subscript 'update_ibi_single.sh' (from tags update ibi_single) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p'
Update potential SNa-SC2 : yes
Running subscript 'resample_target.sh SNa-SC2.tgt SNa-SC2.dist.tgt' (from tags
resample target) dir /home/arice3/Programs/votca/share/votca/scripts/inverse
Running critical command 'mktemp SNa-SC2.dist.tgt_smooth.XXXXX'
Running critical command 'csg_resample --in /local/VOTCA/IBI_test/SNa-SC2.tgt
--out SNa-SC2.dist.tgt_smooth.PP6mM --grid 0.15:0.002:0.45 --comment Created on
Wed Mar 14 14:36:46 CDT 2018 by arice3@mead
called from resample_target.sh, version 1.5-dev gitid: 65d1f9c
settings file: '/local/VOTCA/IBI_test/settings.xml'
working directory: /local/VOTCA/IBI_test/step_001'
Running critical command 'mktemp SNa-SC2.dist.tgt_extrapolated.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 1
--region leftright SNa-SC2.dist.tgt_smooth.PP6mM
SNa-SC2.dist.tgt_extrapolated.w36Sf' (from tags table extrapolate) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 0
table_extrapolate.pl: extrapolating the right using linear with gradient 0
Running subscript 'dist_adjust.pl SNa-SC2.dist.tgt_extrapolated.w36Sf
SNa-SC2.dist.tgt' (from tags dist adjust) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
Running subscript 'update_ibi_pot.pl SNa-SC2.dist.tgt SNa-SC2.dist.new
SNa-SC2.pot.cur SNa-SC2.dpot.pure_ibi 2.49435' (from tags update ibi_pot) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
Running subscript 'potential_shift.pl --type bond SNa-SC2.dpot.pure_ibi
SNa-SC2.dpot.new' (from tags potential shift) dir
/home/arice3/Programs/votca/share/votca/scripts/inverse
No valid value found in SNa-SC2.dpot.pure_ibi at
/home/arice3/Programs/votca/share/votca/scripts/inverse/potential_shift.pl line
87.
Callstack:
/home/arice3/Programs/votca/share/votca/scripts/inverse/inverse.sh - linenumber
264
do_external - linenumber 176 in
/home/arice3/Programs/votca/share/votca/scripts/inverse/functions_common.sh
/home/arice3/Programs/votca/share/votca/scripts/inverse/update_ibi.sh -
linenumber 32
for_all - linenumber 22 (see 'csg_call --cat function for_all')
do_external - linenumber 19 (see 'csg_call --cat function
do_external')
/home/arice3/Programs/votca/share/votca/scripts/inverse/update_ibi_single.sh -
linenumber 42
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/arice3/Programs/votca/share/votca/scripts/inverse/potential_shift.pl
--type bond SNa-SC2.dpot.pure_ibi SNa-SC2.dpot.new #
# (from tags potential shift) failed
#
# For details see the logfile /local/VOTCA/IBI_test/inverse.log
#
#
#
#################################################################################################################################
die: (called from 16487) CSG_MASTER_PID is 12694
die: pids to kill: 12694 15891 16472 16487
