On Sat, Oct 29, 2022 at 10:14 Victor Nazarychev <[email protected]> wrote:
> 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? > it has been a long time , but if I remember correctly the wjk correction was only derived for a single component system. You would have to extend the calculation for multi-component system. I assume it would just map to the partial pressures. Christoph > > > 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. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/7b0e33aa-f7c6-49f4-8818-492374177dc9n%40googlegroups.com > <https://groups.google.com/d/msgid/votca/7b0e33aa-f7c6-49f4-8818-492374177dc9n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- Christoph Junghans Web: http://www.compphys.de -- 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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