On Wed, Oct 19, 2022 at 13:00 Sanjeet Singh <[email protected]> wrote:
> Hello Christoph, > > Sorry for the incessant questioning. > > I got the point that csg_inverse will do the extension automatically. But > when I am using Boltzmann Inversion (not IBI) to get the bonded potential, > then do I need to do the modifications (extending the range of the > potential) manually by using the post-processing tools in VOTCA? Or can I > use csg_inverse for simple Boltzmann Inversion also? > yes, when you do BI then you need to do it manually! Of course you can do IBI for just one step and steal the potential from there ;-) Christoph > Thank you. > > Sanjeet > > > > On Wednesday, October 19, 2022 at 12:17:04 PM UTC-4 Christoph Junghans > wrote: > >> On Wed, Oct 19, 2022 at 9:24 AM Sanjeet Singh <[email protected]> >> wrote: >> > >> > Dear Christoph, >> > >> > I would like to ask a follow-up question to this. Now, suppose I set my >> min = 0.351 and max = 0.367, then I will be getting my potential in this >> range. What if I want to extend my potential outside this range, Say for >> example the range of my dist.tgt file. The range of my dist.tgt file is >> 0.347465 to 0.371461. It's just that in the boundary regions of dist.tgt >> file I don't have a proper sampling. >> >> csg_inverse would to the extension automatically, for manually >> modification see: >> >> https://www.votca.org/csg/preparing.html?highlight=extrapolate#post-processing-of-the-potential >> >> Christoph >> > >> > On Wednesday, October 19, 2022 at 9:05:53 AM UTC-4 Christoph Junghans >> wrote: >> >> >> >> On Tue, Oct 18, 2022 at 6:30 PM Sanjeet Singh <[email protected]> >> wrote: >> >> > >> >> > Hello Christoph, >> >> > >> >> > Thank you for your prompt response. But, I am not able to follow you >> when you say "for csg_botlzmann it doesn't really matter". >> >> What I meant there was that csg_boltzmann will invert things either >> >> way, but what I would do is to pick min and max inside the peak of the >> >> distribution, so 0.351 and 0.367, as you suggested, should work. >> >> >> >> Christoph >> >> >> >> > >> >> > For example in my dist.tgt file here, I have initial data points as >> follows: >> >> > >> >> > 0.347465 0.00833478 >> >> > 0.347705 0.00833478 >> >> > 0.347945 0.0166696 >> >> > 0.348185 0 >> >> > 0.348425 0.00833478 >> >> > >> >> > Therefore, when I am using this dist.tgt file to get bonded >> potential using Boltzmann Inversion I am setting the min at 0.348425 as >> before this I am having a point with zero probability. >> >> > >> >> > Or if I set my min at the starting point 0.347465, then will this be >> OK? >> >> > >> >> > >> >> > On Tuesday, October 18, 2022 at 6:30:42 PM UTC-4 Christoph Junghans >> wrote: >> >> >> >> >> >> On Tue, Oct 18, 2022 at 12:43 PM Sanjeet Singh <[email protected]> >> wrote: >> >> >> > >> >> >> > Hello Christoph, >> >> >> > >> >> >> > I have run a 1000 ns atomistic vacuum simulation to get bonded >> distribution with exclusions obtained using the following command: >> >> >> > >> >> >> > csg_boltzmann --top topology.xml --cg mapping.xml --excl >> exclusions.txt >> >> >> > >> >> >> > Then, I am getting my bonded distribution using the following >> command: >> >> >> > >> >> >> > csg_boltzmann --top topology.xml --trj Trajectory2.dump --cg >> PEO-10.xml --first-frame 500000 < boltzmann_cmds_dist >> >> >> > >> >> >> > After getting my bonded distribution I want to use Boltzmann >> Inversion to get my bonded potential using the following command: >> >> >> > >> >> >> > csg_boltzmann --top topology.xml --trj Trajectory2.dump --cg >> PEO-10.xml --first-frame 500000 < boltzmann_cmds >> >> >> > >> >> >> > Now, suppose I want to do the Boltzmann Inversion for a Bond-AB >> for which I am using the boltzmann_cmds file with the following options: >> >> >> > >> >> >> > tab set T 300 >> >> >> > tab set scale bond #SCALING IS NEEDED TO GET THE VOLUME >> NORMALIZED DISTRIBUTION FUNCTION i.e. dividing the distribution by 4pir^2 >> >> >> > tab set auto 0 >> >> >> > tab set min ______ >> >> >> > tab set max _____ >> >> >> > tab set n 100 >> >> >> > tab bond-AB.potential-file-100.ib *bond-AB* >> >> >> > >> >> >> > Then in the above lines, what should be the value of min and max? >> >> >> > >> >> >> > I am attaching the bonded distribution file for BOND-AB here, and >> also the plot of BOND-AB distribution. >> >> >> > >> >> >> > If I go by the BOND-AB distribution file, then maybe I can use >> min = 0.348425, and max = 0.369061. As before this min and after the max >> value, I have 0 probability for some bond length. >> >> >> > >> >> >> > Or, should I select min and max from the plot of the >> distribution? And select min = 0.351, and max = 0.367, i.e. the range where >> I have the normal distribution in the plot. >> >> >> Short answer is for csg_botlzmann it doesn't really matter. >> >> >> However, for csg_inverse the min and max matter, so the boltzmann >> >> >> inversion from the target distribution (<name>.dist.tgt) is done >> >> >> correctly, if you don't provide an initial guess for the potential >> >> >> (<name>.pot.in) >> >> >> >> >> >> Christoph >> >> >> >> >> >> > >> >> >> > Thank you. I would appreciate any advice you have for me. >> >> >> > >> >> >> > >> >> >> > -- >> >> >> > 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/6187e55a-2925-4a5c-992e-8f3c44112b1bn%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/60ada3ad-6d4f-473c-91ca-1a703f12891en%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/86dd6512-6372-4061-a1d8-130f429ebc6fn%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/96264f49-d275-440a-9ee3-76dece6c69ecn%40googlegroups.com > <https://groups.google.com/d/msgid/votca/96264f49-d275-440a-9ee3-76dece6c69ecn%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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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