Hi,
try to replace:
<post_update>smooth</post_update>
<post_update>pressure</post_update>
by
<post_update>smooth pressure</post_update>
Cheers,
Christoph
Am 8. November 2011 16:32 schrieb Sacha Mould <sacha...@gmail.com>:
> Hi all,
>
> it seems that i figured it out. In my initial script i was calling two
> post-updates, 'smooth' and 'pressure':
>
> <post_update>pressure</post_update>
> <post_update_options>
> <pressure>
> <type>simple</type>
> <do>0 0 1</do>
> <simple>
> <scale>0.37415295</
> scale>
> </simple>
> </pressure>
> </post_update_options>
> <post_update>smooth</post_update>
> <post_update_options>
> <smooth>
> <iterations>2</iterations>
> </smooth>
> </post_update_options>
>
> In this case, the simulation will run, but only the 'smooth' post-
> update will perform and the 'pressure correction will be ignored. In
> case i change the order and put the pressure correction after the
> smooth, the simulation will through me the error that i posted on the
> earlier message. So, i decided to put both of them between the same
> <post-update-options> section, like this:
>
> <post_update_options>
> <smooth>
> <iterations>2</iterations>
> </smooth>
> <pressure>
> <type>wjk</type>
> <do>1 0 0</do>
> <wjk>
> <scale>-0.355861028</scale>
> </wjk>
> </pressure>
> </post_update_options>
>
> In that case, the pressure correction will be performed without a
> problem, but the smoothing fails. If i again change the order of them,
> this time putting the pressure post-update first, smoothing will be
> performed and pressure correction will fail. It seems that i can't
> call those two post-updates, because votca will only accept one of
> them, usually the one that is assigned at last.
>
> Many regards,
>
> Sacha
>
>
>
> On Nov 8, 7:43 pm, Victor Ruehle <rue...@votca.org> wrote:
>> Hmm, looks alright to me. I vaguely remember there was a bug in
>> pressure correction which christoph fixed middle of october. How old
>> is your installation? An upgrade might help....
>>
>> http://csg.votca.googlecode.com/hg-history/default/share/scripts/inve...
>> is the newest one, you could compare with your votca installation in
>> <votca-path>/share/scripts/inverse/pressure_cor_simple.pl
>>
>> Victor
>>
>> 2011/11/8 Sacha Mould <sacha...@gmail.com>:
>>
>>
>>
>>
>>
>>
>>
>> > Hi Sebastian,
>>
>> > sure i can share my script. In this case i'm using only one type of
>> > bonded interaction (B-B). All the beads are the same, with the same
>> > mass. Here it goes the script:
>>
>> > <cg>
>> > <non-bonded>
>> > <name>B-B</name>
>> > <type1>B</type1>
>> > <type2>B</type2>
>> > <min>0</min>
>> > <max>1.5</max>
>> > <step>0.001</step>
>> > <inverse>
>> > <target>B-B.dist.tgt</target>
>> > <do_potential>0 1 0</do_potential>
>> > <post_update>pressure</post_update>
>> > <post_update_options>
>> > <pressure>
>> > <type>simple</type>
>> > <do>0 0 1</do>
>> > <simple>
>> > <scale>0.37415295</scale>
>> > </simple>
>> > </pressure>
>> > </post_update_options>
>> > <post_update>smooth</post_update>
>> > <post_update_options>
>> > <smooth>
>> > <iterations>2</iterations>
>> > </smooth>
>> > </post_update_options>
>> > <post_update_options></post_update_options>
>> > <post_add>convergence</post_add>
>> > <post_add_options></post_add_options>
>> > <p_target>1</p_target>
>> > <particle_dens>3.2965079</particle_dens>
>> > <gromacs>
>> > <table>table_B_B.xvg</table>
>> > </gromacs>
>> > </inverse>
>> > </non-bonded>
>> > <inverse>
>> > <kBT>3.55861028</kBT>
>> > <program>gromacs</program>
>> > <gromacs>
>> > <equi_time>10</equi_time>
>> > <table_bins>0.001</table_bins>
>> > <pot_max>1000000</pot_max>
>> > <table_end>2.5</table_end>
>> > <temp_check>no</temp_check>
>> > <cutoff_check>no</cutoff_check>
>> > </gromacs>
>> > <filelist>grompp.mdp topol.top table.xvg table_a1.xvg
>> > table_b1.xvg
>> > index.ndx</filelist>
>> > <iterations_max>500</iterations_max>
>> > <convergence_check>default</convergence_check>
>> > <convergence_check_options>
>> > <limit>0.001</limit>
>> > <name_glob>*.conv</name_glob>
>> > </convergence_check_options>
>> > <method>ibi</method>
>> > <log_file>inverse.log</log_file>
>> > <restart_file>restart_points.log</restart_file>
>> > </inverse>
>> > </cg>
>>
>> > Thanks a lot,
>>
>> > Sacha
>>
>> > On Nov 8, 7:07 pm, frit...@mpip-mainz.mpg.de wrote:
>> >> Hi Sascha,
>>
>> >> if I am not mistaken, I think you have to set the pressure correction
>> >> for each non-bonded interaction you are using. From your output it
>> >> seems to work for A-A, but fail for A-B and B-B interactions. Try to
>> >> set the other two as well. If it still doesent work, please share your
>> >> full settings.xml file with us. If what I wrote helps, it seems to be
>> >> indeed a bug as it should be possible to pressure correct selected
>> >> interactions.
>>
>> >> Cheers
>> >> Sebastian
>>
>> >> > Hey Victor,
>>
>> >> > i put the pressure section in the <non-bonded> section of <inverse>
>> >> > and p_target is well written. I've tried now to run wjk pressure
>> >> > correction instead... same problem... but the strange thing is that
>> >> > when i set wjk votca tries to run 'pressure_cor_simple.pl' instead of
>> >> > 'pressure_cor_wjk.pl':
>>
>> >> > Energy Average Err.Est. RMSD Tot-Drift
>> >> > -------------------------------------------------------------------------------
>> >> > Pressure 169.74 0.51 57.1507 1.25074
>> >> > (bar)
>> >> > New pressure 169.74
>> >> > an error occurred:
>> >> > property not found: pressure
>> >> > an error occurred:
>> >> > property not found: pressure
>> >> > Apply simple pressure correction for interaction B-B
>> >> > Running subscript 'pressure_cor_simple.pl 169.74 B-
>> >> > B.pressure_correction'(from tags pressure_cor simple)
>> >> > csg_get_interaction_property: csg_property failed on getting value
>> >> > inverse.post_update_options.pressure.simple.scale and no default given
>> >> > ##########################################################################################################################################################################
>> >> > #
>> >> > #
>> >> > #
>> >> > ERROR:
>> >> > #
>> >> > # do_external: subscript /home/lusiterrae/votca/share/votca/scripts/
>> >> > inverse/pressure_cor_simple.pl 169.74 B-B.pressure_correction (from
>> >> > tags pressure_cor simple) failed #
>> >> > #
>> >> > #
>> >> > ######################################################################################################################
>>
>> >> > I'm using Votca last release.
>>
>> >> > Is there any possibility of being a bug?
>>
>> >> > Many regards,
>>
>> >> > Sacha
>>
>> >> > On Nov 8, 4:02 pm, Victor Ruehle <rue...@votca.org> wrote:
>> >> >> Hey,
>>
>> >> >> hmm, error message seems a bit misleading here. Did you put it in the
>> >> >> sub tag <inverse> in non-bonded? so full path is
>> >> >> cg.non-bonded.inverse.post_update_options.pressure.simple.scale
>> >> >> and
>> >> >> cg.non-bonded.inverse.p_target
>>
>> >> >> be aware the _, not - in p_target
>>
>> >> >> Best,
>> >> >> Victor
>>
>> >> >> 2011/11/8 Sacha Mould <sacha...@gmail.com>:
>>
>> >> >> > Hi all,
>>
>> >> >> > i'm trying to use simple pressure correction on my coarse-grained
>> >> >> > simulation but it seems that i'm having some troubles to set it up.
>> >> >> > After the first IBI iteration while votca is doing the post-updates
>> >> >> > and error appears. This is what is written on the last lines of the
>> >> >> > log file:
>>
>> >> >> > Energy Average Err.Est. RMSD Tot-Drift
>>
>> >> >> -------------------------------------------------------------------------------
>> >> >> > Pressure 168.538 1.5 58.0002 -0.923779
>> >> >> > (bar)
>> >> >> > New pressure 168.538
>> >> >> > an error occurred:
>> >> >> > property not found: pressure
>> >> >> > an error occurred:
>> >> >> > property not found: pressure
>> >> >> > Apply simple pressure correction for interaction B-B
>> >> >> > Running subscript 'pressure_cor_simple.pl 168.538 B-
>> >> >> > B.pressure_correction'(from tags pressure_cor simple)
>> >> >> > csg_get_interaction_property: csg_property failed on getting value
>> >> >> > inverse.post_update_options.pressure.simple.scale and no default
>> >> >> > given
>>
>> >> >> ###########################################################################################################################################################################
>> >> >> > #
>> >> >> > #
>> >> >> > #
>> >> >> > ERROR:
>> >> >> > #
>> >> >> > # do_external: subscript /home/lusiterrae/votca/share/votca/scripts/
>> >> >> > inverse/pressure_cor_simple.pl 168.538 B-B.pressure_correction (from
>> >> >> > tags pressure_cor simple) failed #
>> >> >> > #
>> >> >> > #
>>
>> >> >> ###########################################################################################################################################################################
>>
>> >> >> > On the non-bonded interaction section of the settings file i'm
>> >> >> > assigning:
>>
>> >> >> > <post_update>pressure</post_update>
>> >> >> > <post_update_options>
>> >> >> > <pressure>
>> >> >> > <type>simple</type>
>> >> >> > <do>0 0 1</do>
>> >> >> > <simple>
>> >> >> >
>> >> >> > <scale>0.35586102</scale>
>> >> >> > </simple>
>> >> >> > </pressure>
>> >> >> > </post_update_options>
>>
>> >> >> > In addition, i'm assigning <p-target>1</p-target>.
>>
>> >> >> > I wonder what could be missing???
>>
>> >> >> > Thanks a lot in advance.
>>
>> >> >> > Sacha
>>
>> >> >> > --
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>> read more »
>
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