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giorginolab / vmd_diffusion_coefficient

Computing Diffusion Coefficients in Macromolecular Simulations: The Diffusion Coefficient Tool for VMD
https://doi.org/10.21105/joss.01698
BSD 3-Clause "New" or "Revised" License
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calculating diffusion coefficient from linear fit #6

Closed jrperilla closed 4 years ago

jrperilla commented 4 years ago

While using the GUI implementation, and selecting either of the two ‘Plot’ options, it would be beneficial to always output the diffusion coefficient from linear fit to stdout. Since the MSD calculation is expensive, I don’t see a reason not to perform the linear fit and extract the coefficient before calling the Multiplot window, even if the user did not click the separate “Diffusion coefficient from linear fit” button which launches the complete routine anyway but does not plot the MSD.

tonigi commented 4 years ago

Indeed the button was more a "cosmetic" choice to highlight the fact that a fit was taking place. Good point though. I changed the GUI according to the suggestion - the button is gone; D from fit is now implicitly printed and added to the plots. 46a63521cb291a130b32972ddf43082ba316420e