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>smooth</post_update>
<post_update>pressure</post_update>
<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 <[email protected]> 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 <[email protected]>:
>
>
>
>
>
>
>
> > 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, [email protected] 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 <[email protected]> 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 <[email protected]>:
>
> >> >> > 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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