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. 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.
bond-AB.dist-rdf.tgt
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