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".
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.
