On Thu, Nov 10, 2022 at 5:01 AM Victor Nazarychev <[email protected]> wrote: > > Dear Cristoph, > > Thank you for your help. > > среда, 9 ноября 2022 г. в 22:52:45 UTC+3, Christoph Junghans: >> >> On Wed, Nov 9, 2022 at 11:48 AM Victor Nazarychev <[email protected]> wrote: >> > >> > Dear Votca users, >> > >> > I try to parametrize the non-bonded intecations in CG model using the ibi >> > procedure for graphene molecules. However, when I build nanocomposite >> > comprises polymer and graphene flakes is atomostic simulation stacks are >> > formed between the graphene flakes. In this case, the target pair >> > distribution function between CG atoms in graphene falls to 1 only on the >> > end of box. please see the attached file. >> > >> > If I undesrtand it is imposible to acurate calculate potential between the >> > atoms in stacks using ibi procedure due to the fact the rdf does not fall >> > to one. >> There are re-weighting techniques for these kind of systems, e.g. see >> https://doi.org/10.1063/1.4742067 >> > I have a couple of clarifying questions. I did not find re-weighting > techniques in the VOTCA, as I understand this approach has not been > implemented yet? Correct and most likely it will never get added. You will have to overwrite the RDF calculator script with something that works for your special case.
> >> >> > However, could I calculate in some case this like potential for CG model >> > with help of the force-matching? >> I think force-matching could work as well. >> > > If I use bonded potentials calculated by the ibi procedure, will calculating > only nonbonded potentials with the help of force-matching be correct for my > model? Or should I parametrize bonded and non-bonded potential together by > means of force-matching? That depends on the system, so I don't know. We mixed IB/IBI with force-matching in this paper http://dx.doi.org/10.1002/mats.201100011 and it worked, but that isn't a guarantee it will work for your system. IBI reproduces the effective PMF while FM reproduces the average force, which is not always the same. Christoph > > Best regards, > Victor > >> >> Christoph >> > >> > Best regards, >> > Victor >> > >> > -- >> > 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/965daf19-3386-4355-8547-e651605e49b8n%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/fc03698e-076d-4702-8a3a-3c956bc3e079n%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/CAHG27e6nbZXSt17gPHgsHnOe8ySouq-1OS2BB4CsgANGwYiBwA%40mail.gmail.com.
