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. 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