From: Kalas, Vasilios (
Date: Sat Aug 02 2014 - 19:13:35 CDT


I had a question regarding the tutorial (unix version) on the Maxwell-Boltzmann Energy Distribution (section 2.2). When I plot the energy.dat file I generate by following the tutorial instructions with the latest version of NAMD (2.9) or the energy.dat file already created in the example output folder, I find that the peak of the distribution has a relative frequency value of 0.08, as opposed to 0.8 as plotted in the tutorial file. This obviously prevents me from adequately fitting a curve to the distribution and extracting the kbT value (using the equation provided in the tutorial). I see the same histogram with the created or existing energy.dat file in different softwares so I know that my plotting of the data is not at fault. This leaves me to believe that the problem lies with the way the distribution is calculated by one of the scripts (energy.tcl) or perhaps some other parameter. Has anyone encountered this problem before (aka 10-fold difference in y axis value)? Any fixes to this problem?

I appreciate your help.

Vasilios Kalas

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