On Thu, Nov 10, 2022 at 7:52 PM Sanjeet Singh <[email protected]> wrote: > > Hello Christoph, > > Thank you for your support and guidance. > > Now, IBI is working for me. And I have already started the pressure > correction step. But, I am not able to stabilize the pressure in my system, > which is fluctuating a lot. Can you please point out the reason why is it so? That is very common, I would try to scale down the update from the pressure correction.
> > I am hereby attaching my settings.xml file, and the lammps.pressure file > after 50 iterations. > > I would also like to know that is it ok to perform the potential update and > pressure correction at the same step of the iteration? That depends on the system, but I wouldn't do it at the same time. > > Also, what is the unit of p_target in the settings.xml file? It is the same units as whatever your MD program prints out. Christoph > > Thank you. > > Sanjeet > > On Wednesday, November 9, 2022 at 11:26:33 PM UTC-5 Christoph Junghans wrote: >> >> 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. > > -- > 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/2abd0c38-3ec0-4d20-9b77-2573aca1c4een%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. 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