Dear Cristoph, Thank you very much.
Victor воскресенье, 30 октября 2022 г. в 20:26:38 UTC+3, Christoph Junghans: > 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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