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Update mda_COG.ipynb
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jd15489 committed Nov 21, 2023
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"source": [
"# Diffusion coefficient of molecules using center of mass\n",
"\n",
"`kinisi` includes the ability to calculate the mean-squared displacement and diffusion coefficient of the center of mass (or geometry) of molecules. This can be done for a single molecule or a collection of molecules. It is important to note that inclusion of rotational motion in the calcuation of diffusion coeffiencents can lead to erronious results. This rotation can be elminated from the calculation by taking the center of mass for each molecule.\n",
"`Kinisi` includes the ability to calculate the mean-squared displacement and diffusion coefficient of the center of mass (or geometry) of molecules. This can be done for a single molecule or a collection of molecules. It is important to note that inclusion of rotational motion in the calcuation of diffusion coeffiencents can lead to erronious results. This rotation can be elminated from the calculation by taking the center of mass for each molecule.\n",
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