Hi,
I am trying to run the thermoforce correction for a custom solvent+molecule
system. I am using basically the same settings.xml as of the spce/tf
tutorial of VOTCA 1.2.3. I can run the tutorial without problems, but when
I try to do the same on another system, I have two issues:
1) What is the actual meaning of the following settings.xml parameters and
how do I calculate them for my own system?
<!-- thermodynmic force: apply in this range -->
<min>1.4</min>
<max>3.1</max>
<step>0.01</step>
<!--spline:offset beyond the hyrbid zone to take into account for
fitting the spline-->
<tf>
<spline_start>0.9</spline_start>
<spline_end>3.6</spline_end>
<spline_step>0.4</spline_step>
<molname>SOL</molname>
<prefactor>0.01382</prefactor>
</tf>
2) When I try to calculate the thermoforce correction, csg_inverse stops
immediately with the following error (from inverse.log):
------------------------
Prepare (dir step_000)
------------------------
cp_from_main_dir: 'adress_spce.itp grompp.mdp topol.top table.xvg index.ndx
table_XX_XX.xvg'
Running critical command 'pushd
/home/massimo/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce'
~/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce
~/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/step_000
Running critical command 'cp adress_spce.itp grompp.mdp topol.top table.xvg
index.ndx table_XX_XX.xvg
/home/massimo/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/step_000'
Running critical command 'popd'
~/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/step_000
Running subscript 'prepare_generic.sh' (from tags prepare tf) dir
/home/massimo/gromacs/votca/votca/share/votca/scripts/inverse
For all bonded
For all non-bonded
for_all: run 'do_external prepare_single tf'
Running subscript 'prepare_generic_single.sh' (from tags prepare_single tf)
dir /home/massimo/gromacs/votca/votca/share/votca/scripts/inverse
Using initial guess from dist dens.SOL.xvg for SOL
cp_from_main_dir: 'dens.SOL.xvg' to 'SOL.dist.tgt'
Running critical command 'pushd
/home/massimo/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce'
~/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce
~/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/step_000
Running critical command 'cp dens.SOL.xvg
/home/massimo/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/step_000/SOL.dist.tgt'
Running critical command 'popd'
~/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/step_000
Running critical command 'mktemp -u SOL.pot.new.raw.XXX'
Running subscript 'calc_thermforce.sh SOL.dist.tgt SOL.pot.new.raw.jn0'
(from tags calc thermforce) dir
/home/massimo/gromacs/votca/votca/share/votca/scripts/inverse
an error occurred:
property not found: tf
Callstack:
/home/massimo/gromacs/votca/votca/share/votca/scripts/inverse/inverse.sh -
linenumber 166
do_external - linenumber 170 in
/home/massimo/gromacs/votca/votca/share/votca/scripts/inverse/functions_common.sh
/home/massimo/gromacs/votca/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')
/home/massimo/gromacs/votca/votca/share/votca/scripts/inverse/prepare_generic_single.sh
- linenumber 53
do_external - linenumber 18 (see 'csg_call
--cat function do_external')
/home/massimo/gromacs/votca/votca/share/votca/scripts/inverse/calc_thermforce.sh
- linenumber 57
csg_get_interaction_property -
linenumber 79 (see 'csg_call --cat function csg_get_interaction_property')
die - linenumber 2 (see 'csg_call
--cat function die')
################################################################################################################################################################################################################################################################################################
#
#
#
ERROR:
#
# csg_get_interaction_property: Could not get 'inverse.tf.spline_start' for
interaction with name 'SOL' from
/home/massimo/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/settings.xml
and no default was found in
/home/massimo/gromacs/votca/votca/share/votca/xml/csg_defaults.xml #
# For details see the logfile
/home/massimo/gromacs/cg-adress-tests/adress-uim-20130108/thermoforce/inverse.log
#
#
#
################################################################################################################################################################################################################################################################################################
die: (called from 4468) CSG_MASTER_PID is 3852
----
Below is settings.xml :
<cg>
<!-- example for a non-bonded interaction entry -->
<non-bonded>
<!-- name of the index group to calculate density from -->
<name>SOL</name>
<!-- types involved in this interaction -->
<!-- thermodynmic force: apply in this range -->
<min>1.4</min>
<max>3.1</max>
<step>0.01</step>
<!--spline:offset beyond the hyrbid zone to take into account for
fitting the spline-->
<tf>
<spline_start>0.9</spline_start>
<spline_end>3.6</spline_end>
<spline_step>0.4</spline_step>
<molname>SOL</molname>
<prefactor>0.01382</prefactor>
</tf>
<inverse>
<!-- target distribution -->
<target>dens.SOL.xvg</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_update></post_update>
<!-- additional post processing of U after dU added to potential -->
<post_add></post_add>
<!-- name of the table for gromacs run -->
<gromacs>
<table>tabletf.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<!-- general options for inverse script -->
<inverse>
<!-- 300*0.00831451 gromacs units -->
<kBT>2.49435</kBT>
<!-- use gromacs as simulation program -->
<program>gromacs</program>
<!-- gromacs specific options -->
<gromacs>
<grompp><bin>grompp_4.6b2</bin>
</grompp>
<mdrun><command>mpirun -np 8 mdrun_4.6b2</command>
<!-- <opts>-nt 8</opts> -->
</mdrun>
<!-- trash so many frames at the beginning -->
<equi_time>0</equi_time>
<!-- grid for table*.xvg !-->
<table_bins>0.01</table_bins>
<!-- cut the potential at this value (gromacs bug) -->
<pot_max>1000000</pot_max>
<!-- extend the tables to this value -->
<table_end>7.1</table_end>
</gromacs>
<!-- these files are copied for each new run -->
<filelist>adress_spce.itp grompp.mdp topol.top table.xvg index.ndx
table_XX_XX.xvg</filelist>
<!-- do so many iterations -->
<iterations_max>300</iterations_max>
<!-- ibi: inverse biltzmann imc: inverse monte carlo tf: thermody force
-->
<method>tf</method>
<!-- directory for user scripts -->
<scriptdir></scriptdir>
<!-- write log to this file -->
<log_file>inverse.log</log_file>
<!-- write restart step to this file -->
<restart_file>restart_points.log</restart_file>
</inverse>
</cg>
----
Thanks!
Massimo
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