On Wed, Nov 9, 2022, 20:27 Sanjeet Singh <[email protected]> wrote:
> Dear Christoph, > > Thank you for your response. > > I have some doubt regarding the post_update_options.scale. I have six > types of non-bonded interaction in my system and I want to update them at > the same iteration step, then shall I use the scale factor as 1/6 (0.167) > approximately for each of them? > > Similarly, for the post_update_options.pressure.simple.scale, if I want to > update all of my six interaction at the same step, then what should be the > value of the scale factor? > > I mean if it is related to the compressibility of the system, then if my > polymer has a compressibility value of 1. Then, what should be the value of > the scale factor for each of my interaction. Will it be again 1/6? > > Or, how to decide upon the weightage I can give to each of the six > interactions with respect to the scale factor for pressure update? > > Can it be related to the fraction of each bead in my system? Or, the bead > with higher fraction will have higher weightage? > I could now speculate, but the short answer is, I don't know! All these things are very system-specific and you will have figure it out by try and error. My only advice is too not try too many things at once. Get IBI to work then add pressure correction etc. Sorry, Christoph > Thank you. > > Sanjeet > > On Tuesday, November 8, 2022 at 10:04:02 PM UTC-5 Christoph Junghans wrote: > >> 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/1c62f79e-e530-4d33-9b50-a81cbe95dd34n%40googlegroups.com > <https://groups.google.com/d/msgid/votca/1c62f79e-e530-4d33-9b50-a81cbe95dd34n%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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