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/inverse/pressure_cor_simple.pl 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 >> >> >> > -- >> >> > You received this message because you are subscribed to the >> >> Google Groups "votca" group. >> >> > To post to this group, send email to [email protected]. >> >> > To unsubscribe from this group, send email to >> >> [email protected]. >> >> > For more options, visit this group >> >> athttp://groups.google.com/group/votca?hl=en. >> >> > -- >> > You received this message because you are subscribed to the Google >> > Groups "votca" group. >> > To post to this group, send email to [email protected]. >> > To unsubscribe from this group, send email to >> > [email protected]. >> > For more options, visit this group at >> >http://groups.google.com/group/votca?hl=en. >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > > -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
