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?
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 >> <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. > 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 > <https://groups.google.com/d/msgid/votca/CAHG27e6vvXvA5se0FmRiDhsJfMVgkkw%2BLRPQu8fQMtxO6yo8dQ%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- 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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