On Thu, Oct 20, 2022 at 6:25 AM Sanjeet Singh <[email protected]> wrote: > > 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? It seems the grid spacing is different and hence some kind of interpolation and /or spline fitting might have happened during the procedure. (For dihedrals there is even some consideration about the periodicity) Usually VOTCA tells you all the steps it is doing along the way, but without these details it is hard to say for me right now what exactly triggered the difference. If you post the commands you ran and output you got here we can have a look at the details.
On a related note: dihedral interactions are a bit tricky due to periodicity and grid spacing and when you search this mailing list you will find some other cases where VOTCA wasn't smart enough to handle all cases and users had to fail back to manual inversion. Christoph > > 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. >> >> -- >> 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/f954a415-b916-49e7-aace-d7ab2ab41aa6n%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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