Dear Votca users, I have a simple question. It is unclear for me how can I calculate the <particle_dens> for pressure correction. Could you, please, suggest some example, where how this value is calculated? My model is consists of 1000 chains, each chain has 5 CG particles: 2 of type A and 3 of type B. Could you help me, what <particle_dens> values should I use for non-bonded A-A, B-B, and A-B interactions?
Best regards, Victor среда, 9 ноября 2011 г. в 22:26:32 UTC+4, Christoph Junghans: > And yes, this is a bug: < > https://code.google.com/p/votca/issues/detail?id=121> > > Christoph > > Am 9. November 2011 02:52 schrieb Sacha Mould <[email protected]>: > > 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. > > 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. > > > > > > -- > Christoph Junghans > Votca Core Developer > > Web: http://www.votca.org > -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. 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