Hello Saeed Yes, you can also optimize bond and angle potentials such that the distributions match the atomistic simulation. In my experience, optimizing everything at the same time is not ideal, as it can prevent convergence. Optimizing bonded and non-bonded interactions alternately will more likely work. See this tutorial <https://github.com/votca/votca/tree/master/csg-tutorials/hexane/ibi_all> and the `do_potential` option.
Cheers, Marvin On Monday, 19 December 2022 at 14:27:19 UTC+1 [email protected] wrote: > Dear Christoph, > > I appreciate your help. > My AA RDF was not correct now it works and the CG RDF matches with AA. I > have another question, the RDF for non-boned is matched and I did a > pressure correction also to have the correct pressure and density. But the > distribution bond, angle, and dihedral do not match with the target > all-atom model. should I do the ibi for bonded interactions also? if so, > should I first do the iteration for bonded interaction and then for > nonbonded or vice versa? or at the same time? > > Best regards > Saeed > > > > On Fri, Nov 18, 2022 at 8:36 PM Christoph Junghans <[email protected]> > wrote: > >> On Fri, Nov 18, 2022 at 11:55 AM Saeed Norouzi <[email protected]> >> wrote: >> > >> > Dear Christoph, >> > >> > Thank you for your reply, I tried those but did not work, and still, >> the RDF increases during ibi iteration. >> Maybe I am misunderstanding, but your target RDF doesn't go to 1.0, >> which has nothing to do with IBI or VOTCA. >> >> Christoph >> >> > >> > Best regards >> > Saeed >> > >> > On Fri, Nov 18, 2022 at 5:02 PM Christoph Junghans <[email protected]> >> wrote: >> >> >> >> On Fri, Nov 18, 2022 at 7:19 AM Saeed Norouzi <[email protected]> >> wrote: >> >> > >> >> > Dear developers, >> >> > >> >> > I am trying to run IBI using csg_inverse --options settings.xml, and >> all necessary information is attached below. my RDF does not go to 1 during >> ibi iteration. Can you please help me with what is wrong? >> >> Looks to me like you need to increase the box size and just sample the >> >> RDF to a higher radius. (in the target setup) >> >> Also a step of 0.005 seems a bit too fine, try 0.01 as a start, only >> >> make it finer if you can resolve a peak. >> >> >> >> Christoph >> >> >> >> > >> >> > -- >> >> > 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/7f17c7ad-8b77-401d-ac20-6355dc20d42an%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 a topic in the >> Google Groups "votca" group. >> >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/votca/iOTPmIL_RVA/unsubscribe. >> >> To unsubscribe from this group and all its topics, send an email to >> [email protected]. >> >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAHG27e64kEi1TgPEzQNkU4r%2BXEHNpZjMro7mSZnjF86GoNc6Fw%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/CAJZjMJY%3D1-e6YCrrSTr-QK36QOgJVQ5ofzeqPy7Z4qbda9hidg%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. >> 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/CAHG27e52R0GuQFSt1rcRO2jZJTxSyq_DSDJJ_k3XLviCVL-VfA%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/74170c2d-5cac-48c8-aae1-855a732a47bdn%40googlegroups.com.
