calc thermforce calc_thermforce.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 get cma_get.sh
cma precede_state cma_processor.py
calc target_rdf calc_target_rdf_generic.sh
pressure_cor simple pressure_cor_simple.pl
pressure_cor wjk pressure_cor_wjk.pl
kbibi ramp_correction kbibi_ramp_correction.pl
calc kbint calc_kbint.sh
density symmetrize density_symmetrize.py
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 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
configuration compare configuration_compare.py
tables jackknife tables_jackknife.pl
run gromacs run_gromacs.sh
presimulation gromacs run_gromacs.sh --pre
pressure gromacs calc_pressure_gromacs.sh
rdf gromacs calc_rdf_generic.sh
imc_stat gromacs imc_stat_generic.sh
density gromacs calc_density_gromacs.sh
prepare_generic gromacs prepare_generic_gromacs.sh
initstep_generic gromacs initialize_step_generic_gromacs.sh
prepare_generic espresso prepare_generic_espresso.sh
initstep_generic espresso initialize_step_generic_espresso.sh
convert_potential gromacs potential_to_gromacs.sh
convert_potential xvg table_to_xvg.pl
functions gromacs functions_gromacs.sh
run espresso run_espresso.sh
pressure espresso calc_pressure_espresso.sh
rdf espresso calc_rdf_espresso.sh
convert_potential espresso potential_to_espresso.sh
convert_potential tab table_to_tab.pl
functions espresso functions_espresso.sh
------------------------
Prepare (dir step_000)
------------------------
cp_from_main_dir: 'grompp.mdp topol.top table_C_C.xvg table_a1.xvg
table_b1.xvg table_d1.xvg index.ndx'
Running critical command 'pushd /home/valentina/CG'
~/CG ~/CG/step_000
Running critical command 'cp grompp.mdp topol.top table_C_C.xvg
table_a1.xvg table_b1.xvg table_d1.xvg index.ndx
/home/valentina/CG/step_000'
Running critical command 'popd'
~/CG/step_000
Running subscript 'prepare_generic.sh' (from tags prepare ibi) dir
/share/apps/votca/share/votca/scripts/inverse
For all bonded
for_all: run 'do_external prepare_single ibi'
Running subscript 'prepare_generic_single.sh' (from tags prepare_single
ibi) dir /share/apps/votca/share/votca/scripts/inverse
Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p'
Using given table CC.pot.in for CC
Running critical command 'mktemp CC.pot.in.smooth.XXX'
Converting /home/valentina/CG/CC.pot.in to CC.pot.new
Running critical command 'csg_resample --in /home/valentina/CG/CC.pot.in
--out CC.pot.in.smooth.sU6 --grid 0:0.01:4 --comment Created on Wed Oct 17
17:42:27 BST 2012 by [email protected]
called from prepare_generic_single.sh, version 1.3-dev hgid: cae513aba385
settings file: /home/valentina/CG/settings.xml
working directory: /home/valentina/CG/step_000'
Running critical command 'mktemp CC.pot.in.extrapolate.XXX'
Running subscript 'potential_extrapolate.sh --type CC.pot.in.smooth.sU6
CC.pot.in.extrapolate.YdY' (from tags potential extrapolate) dir
/share/apps/votca/share/votca/scripts/inverse
Callstack:
/share/apps/votca/share/votca/scripts/inverse/inverse.sh - linenumber 166
do_external - linenumber 170 in
/share/apps/votca/share/votca/scripts/inverse/functions_common.sh
/share/apps/votca/share/votca/scripts/inverse/prepare_generic.sh -
linenumber 31
for_all - linenumber 17 (see 'csg_call --cat function for_all')
do_external - linenumber 18 (see 'csg_call --cat
function do_external')
/share/apps/votca/share/votca/scripts/inverse/prepare_generic_single.sh -
linenumber 43
do_external - linenumber 18 (see 'csg_call
--cat function do_external')
/share/apps/votca/share/votca/scripts/inverse/potential_extrapolate.sh -
linenumber 64
die - linenumber 2 (see 'csg_call --cat
function die')
################################################################################################################################
#
#
#
ERROR:
#
# potential_extrapolate.sh: please specify add potential type (--type
options) from: non-bonded bond thermforce angle dihedral #
# For details see the logfile
/home/valentina/CG/inverse.log
#
#
#
################################################################################################################################
die: (called from 591) CSG_MASTER_PID is 32479
die: pids to kill: 0
On Friday, September 28, 2012 2:07:44 PM UTC+1, Valentina wrote:
>
> Hello!
>
> I am a little confused here.
>
> I have read somewhere that Votca 1.3 (? I thought latest version is 1.2.3)
> supports IBI for bonded - is this right?
>
> If so, how do I implement it? I have attatched my settings file (saved in
> .odt,but used as .xml on the machine). This doesn't seem to do more then
> fitting the nonbonded C-C potential. Am I missing something?
>
> Many thanks!
> Valentina
>
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