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/CAHG27e7e%2ByXaO_MRrjdi4pzeWXg93RWy76TW_nLTWUqfePs2CA%40mail.gmail.com.
