Hi,
thanks for your fast answer!
a change in the output pattern was also my firtst thought.
I first tried gmx version 5.0.4 and encountered the same error. I then
tried it with gmx version 4.6.7 and the same error occured. I compared the
outputs but there is no difference.
I replaced the original commands in calc_pressure_gromacs.sh:
'p_now=$(echo "$output" | sed -n
's/^Pressure[^-0-9]*\(-\?[0-9][^[:space:]]*[0-9]\)[[:space:]].*$/\1/p' ) ||
\
die "${0##*/}: awk failed"
[[ -z $p_now ]] && die "${0##*/}: Could not get pressure from simulation"
with
p_now=$(echo "$output" | sed -n 's/Pressure/&/p' | gawk '{print $2}')
Now the script can read the pressure but the inverse.log shows a couple new
errors:
...
gcq#104: "Count the Bubbles In Your Hair" (The Breeders)
Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 1 data sets
All statistics are over 101 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Pressure 1020.87 5.2 17.5364 -17.3012 (bar)
New pressure 1020.87
an error occurred:
property not found: type
an error occurred:
property not found: do
Apply simple pressure correction for interaction CG-CG
Running subscript 'pressure_cor_simple.pl 1020.87
CG-CG.pressure_correction'(from tags pressure_cor simple)
Use of uninitialized value in concatenation (.) or string at
/Users/jaschonek/votca_gmx_4.6.7/share/votca/scripts/inverse/CsgFunctions.pm
line 161.
Use of uninitialized value in concatenation (.) or string at
/Users/jaschonek/votca_gmx_4.6.7/share/votca/scripts/inverse/CsgFunctions.pm
line 161.
...
My xml file looks like:
<cg>
<!-- example for a non-bonded interaction entry -->
<non-bonded>
<!-- name of the interaction -->
<name>CG-CG</name>
<!-- types involved in this interaction -->
<type1>CG</type1>
<type2>CG</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.25</min>
<max>1.4</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>CG-CG.dist.tgt</target>
<!-- update cycles -->
<do_potential>0 0 1</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_update>pressure</post_update>
<post_update_options>
<pressure>
<simple>
<scale>0.0003</scale>
</simple>
</pressure>
</post_update_options>
<p_target>1</p_target>
<!-- additional post processing of U after dU added to potential -->
<post_add></post_add>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_CG_CG.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>
<!-- trash so many frames at the beginning -->
<equi_time>0</equi_time>
<!-- grid for table*.xvg !-->
<table_bins>0.002</table_bins>
<!-- cut the potential at this value (gromacs bug) -->
<pot_max>1000000</pot_max>
<!-- extend the tables to this value -->
<table_end>3.0</table_end>
</gromacs>
<!-- these files are copied for each new run -->
<filelist>grompp.mdp topol.top table.xvg index.ndx </filelist>
<!-- do so many iterations -->
<iterations_max>10</iterations_max>
<!-- ibi: inverse biltzmann imc: inverse monte carlo -->
<method>ibi</method>
<!-- directory for user scripts -->
<scriptpath></scriptpath>
<!-- 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>
Did I something wrong in the xml-file?
Thanks
Stefan
Am Freitag, 15. Mai 2015 00:22:52 UTC+2 schrieb Christoph Junghans:
>
> Hi,
>
> I am not 100% sure, where the error is.
>
> What exactly did you modify?
>
> You can have a look at calc_pressure_gromacs.sh to see what VOTCA
> actually does, but basically we take the output from g_energy and
> apply a regular expression to grep the pressure, somehow similar to
> what:
> $ g_energy | sed -n
> 's/^Pressure[^-0-9]*\(\(-\?[0-9][^[:space:]]*[0-9]\|nan\)\)[[:space:]].*$/\1/p'
>
>
> would do.
>
> Which gromacs version are you using? As maybe the output pattern has
> changed.
>
> Christoph
>
> 2015-05-14 11:01 GMT-06:00 Stefan Jaschonek <[email protected]
> <javascript:>>:
> > Hallo votca users,
> > I am new to votca and just started course graining a very simple system
> > (ibi). But every time I try to include pressure coupling it fails with
> the
> > message:
> > ERROR: calc_pressure_gromacs.sh: Could not get pressure from
> simulation.
> > The inverse.log-file shows something different: before showing the error
> > message it actually calculates the pressure using g_energy. It seems
> that
> > calc_pressure_gromacs.sh fails to read the pressure because when I
> modify
> > it, it can read the pressure. Is this a bug or is this due to my
> settings?
> > Many thanks in advance
> > Stefan
> >
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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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