Hi Marvin, Thank you for your suggestion.
Best regards Saeed On Mon, Dec 19, 2022 at 2:42 PM Marvin Bernhardt <[email protected]> wrote: > 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 > <https://groups.google.com/d/msgid/votca/74170c2d-5cac-48c8-aae1-855a732a47bdn%40googlegroups.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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