Dear Christoph, Thank you for the clarifications.
I have another question. I was just verifying by hand the bonded potential which we get by using the Simple Boltzmann Inversion method. Say for example for a Dihedral distribution. The first few data points from dist.tgt file is shown below: -3.14159 0.456519 -3.07876 0.897376 -3.01593 0.866437 -2.95309 0.825311 -2.89026 0.760535 Now, for the first data point if I try to get the potential by hand by using the formula *U(q) = -**kBT** ln **P(q), *I am getting the value *1.95587*. But the value which VOTCA gives me is *1.72411.* Can you please explain the reason for this discrepancy? Here are the first few data points from the potential table: -3.14159 1.72411 40.8857 -3.09942 0 20.0311 -3.05725 0.0347262 -1.32404 -3.01508 0.111667 -1.92226 -2.97291 0.196846 -2.01054 Thank you. Sanjeet On Wednesday, October 19, 2022 at 7:02:32 PM UTC-4 Christoph Junghans wrote: > 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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