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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