On Tue, Nov 8, 2022 at 12:05 PM Sanjeet Singh <[email protected]> wrote: > > Hello Christoph, > > I applied all your suggestions and replaced the tabulated bond stretching > potential with the harmonic functional form. And now I am getting somewhat > improved result. Good, I always recommend doing non-bonded only first and then throwing the bonded interactions later.
> > But, again convergence problem is there. Furthermore, at some steps of the > iterations, I found that two beads of my system are in direct contact with > each other. > > Can you please point out the reason for this, and the possible remedy? That is a very system specific question. But I guess you will have to increase the repulsive core of the non-bonded interactions.Check the file <name>.pot (or whatever name you picked in the settings file) in the last step_* directory to see if it is extrapolated/repulsive enough. Usually you can do that by increasing the repulsive core by increasing the <min> of said interaction a bit. Christoph > > I am also attaching snapshots of the simulation box for your reference. > > Thank you. > > Sanjeet > > On Monday, November 7, 2022 at 9:34:22 AM UTC-5 Christoph Junghans wrote: >> >> On Sun, Nov 6, 2022 at 6:47 PM Sanjeet Singh <[email protected]> wrote: >> > >> > Hello Christoph, >> > >> > I am trying to perform IBI for non-bonded interaction. I have 3 bead types >> > in my system. >> > >> > I have already run it for more than 500 iterations, but IBI is not able to >> > reproduce the target distribution. >> > >> > Can you please suggest on how to work on this? >> I look like you don't have enough statistics in each iteration, you >> could do the following: >> - more MD steps >> - decrease the step size - 0.002 seems a bit too small >> - using scale and potential_do will also throw out some of the stats. >> >> Regarding the peak around 0.35nm in the Bead2-Bead2 plot, it seems to >> me you count an intra-moleculde pair there. >> If that is the case, you will need to exclude that. >> You can search the mailing for more details, but in short, just add a >> bond section in your topology.xml (see >> https://github.com/votca/votca/blob/master/csg-tutorials/hexane/atomistic/hexane.xml#L26) >> and use said topology file instead of the data file. >> Inttra molecular interaction will automatically generate exclusion, >> you can check that with: csg_dump --top topology.xml --excl >> >> Christoph >> >> > >> > I am hereby attaching the rdf for two of the non-bonded interactions in my >> > system along with the setting.xml file. >> > >> > Thank you. >> > >> > Sanjeet >> > >> > >> > -- >> > 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/560c96cd-e0f7-4bb7-a339-8e031c1bdab1n%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/9b5b82f3-b37e-45e1-985d-e505c4bc9d2en%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/CAHG27e6dm%3DAqQE12dPT_ao5t%2BoWX1yErKM1gxY3v7hqtR3aybQ%40mail.gmail.com.
