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Update mda_COG.ipynb
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jd15489 committed Nov 20, 2023
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4 changes: 2 additions & 2 deletions docs/source/mda_COG.ipynb
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"id": "9afa4b93-7e49-4a83-9426-fbef4aaf8ecc",
"metadata": {},
"source": [
"We want to calculate the diffusion of the center of mass of the ethene molecule. This can be done by setting `specie` to None and specifying the indices of the molecules of interest in `specie_indices`. To define moelcules, a list of lists should be passed under the `specie_indices` keyword. The outer list has one entry per molecule and each inter list has the indices of that molecule. Only identical molecules are supported. The masses of the atoms in the molecules can be specified with `masses`. This must be a list with the same length as a molecule (the length of one of the inner lists in `specie_indices`)."
"We want to calculate the diffusion of the center of mass of the ethene molecule. This can be done by setting `specie` to None and specifying the indices of the molecules of interest in `specie_indices`. To define molecules, a list of lists should be passed under the `specie_indices` keyword. The outer list has one entry per molecule and each inter list has the indices of that molecule. Only identical molecules are supported. The masses of the atoms in the molecules can be specified with `masses`. This must be a list with the same length as a molecule (the length of one of the inner lists in `specie_indices`)."
]
},
{
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.6"
"version": "3.11.5"
}
},
"nbformat": 4,
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