2015-05-15 3:36 GMT-06:00 Stefan Jaschonek <jascho...@googlemail.com>:
> 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}')
That is strange, because
$ echo "Pressure 1020.87 5.2 17.5364
-17.3012 (bar)" | sed -n
's/^Pressure[^-0-9]*\(-\?[0-9][^[:space:]]*[0-9]\)[[:space:]].*$/\1/p'
returns the pressure for me. Can you try that please?
But from this line above I saw an more important thing, you seem to
use VOTCA 1.2, so please install VOTCA 1.3-dev first , so that we are
sure the issue isn't already fixed in the latest version:
<https://code.google.com/p/votca/wiki/Installing#Development_Version>
Cheers,
Christoph
> 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 <jasc...@googlemail.com>:
>> > 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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