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/CAHG27e7oEPYC02DEcMJ1Mm-1hkskyeNVU5%3DY%2Bw_kCqb7ZV-rXQ%40mail.gmail.com.
