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/CAJZjMJY%3D5p0vmSnx30kJ%2BB3OhWzFoCxSodxpbe%3DGskTRpjYh4A%40mail.gmail.com.
