On Tue, Nov 8, 2022 at 7:23 PM Sanjeet Singh <[email protected]> wrote: > > Dear Christoph, > > In the settings.xml file what should be the value of cg. inverse. kBT, if am > using LAMMPS (real units) as a simulation program as shown below: > > <inverse> > <kBT>2.49435</kBT> > </simulation> > <program>lammps</program> > <!-- lammps specific options --> > > If my T = 300 K, should it be 300 * 0.00198720 = 0.5962 kcal/mol K, or 300 * > 0.0083144621 = 2.49434 kJ/mol K. You should use 0.5962, but honestly it isn't used in my place besides being the prefactor of the update and you already scaled down the update with a factor 0.1 So it shouldn't matter much.
Christoph > > Thank you. > > Sanjeet > On Tuesday, November 8, 2022 at 2:59:36 PM UTC-5 Christoph Junghans wrote: >> >> 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/b36d2e4f-8a2b-48a4-8326-2bf69151d04bn%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/CAHG27e5SKWmMJ-2Jq_y1CWm32LXC7FGWg4FV49D3Mo2ed_XcWA%40mail.gmail.com.
