Hi Christoph, it works!!!! Thanks so much!!!!
All the best, Sacha On Nov 9, 3:19 am, Christoph Junghans <[email protected]> wrote: > 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 <[email protected]>: > > > > > > > > > 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 <[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... > > read more » -- You received this message because you are subscribed to the Google Groups "votca" group. 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