On Sun, Oct 30, 2022 at 10:21 AM Victor Nazarychev <[email protected]> wrote: > > Dear Christoph, > > Thank you very much for your help. I tried to find how to calcualte partial > pressures, but did not find any information about it. Maybe you could suggest > how to calculate partial pressures with Gromacs?
If I remember correctly, gromacs doesn't support partial pressures, but lammps does. Might be more a question for the gromacs mailing list though. We had modified gromacs at some point, but this change never made it upstream. There is a local pressure version in Sikandar's gromacs fork: https://github.com/symashayak/gromacs/tree/release-4-6-1-localpressure_slab But I am not sure that was the right version. Christoph > > Best regards, > Victor > > сб, 29 окт. 2022 г. в 22:17, Christoph Junghans <[email protected]>: >> >> >> >> 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. >> >> -- >> 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. >> 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/CAHG27e6vvXvA5se0FmRiDhsJfMVgkkw%2BLRPQu8fQMtxO6yo8dQ%40mail.gmail.com. > > -- > 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/CALpHq2e-HrmYpd1B_9gWCG-zmxVssKM-nPY7Tsf%3DU1fOB7XezA%40mail.gmail.com. -- 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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