On Fri, Oct 21, 2022 at 7:49 AM Sanjeet Singh <[email protected]> wrote: > > Hello Christoph, > > For calculating the dihedral potential I have just use the following command: > > csg_boltzmann --top topology.xml --trj Trajectory2.dump --cg PEO-10.xml > --first-frame 500000 < boltzmann_cmds > > Where the boltzmann_cmds file I am using is following: > > tab set T 300 > tab set scale no #DIHEDRAL DISTRIBUTION DOESNOT NEED TO BE NORMALIZED > tab set auto 0 > tab set min -3.07876 > tab set max 3.07876 > tab set n 150 > tab dihedral-ABBB.potential.ib *dihedral-ABBB* > > To be on the same page, when I am using the potential of mean force formula > U(q) = -kBT ln P(q), I am using kB value as 0.0083144 kJ/mol K. > > But, I also think that the deviation will be mainly because of the different > grid spacing and some fitting which might have taken place. > > Also, can you please point out What do you mean by manual inversion of the > dihedral interactions? > > I mean after performing the Simple Boltzmann inversion to get the dihedral > potential, postprocessing of the potential should be done manually by running > each command one by one. > Is that what you mean? Yes, sorry I meant the post processing of the potentials, that is described here: https://www.votca.org/csg/preparing.html?highlight=extrapolate#post-processing-of-the-potential
Christoph > > Thank you. > > Sanjeet > > On Thursday, October 20, 2022 at 9:51:33 AM UTC-4 Christoph Junghans wrote: >> >> 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. > 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/9049da08-df98-465c-92cf-dab49c10b434n%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/CAHG27e7ByNTsm14jjGDPeRSBwmFP8oTjYN35RhE88WPu%3DLktQw%40mail.gmail.com.
