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markovmodel / pyemma_tutorials

How to analyze molecular dynamics data with PyEMMA
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[00] add_distances periodic boundaries #103

Closed thempel closed 6 years ago

thempel commented 6 years ago

We need to turn-off the periodic boundaries in the distance computations since the protein was aligned before. We should also mention at some point that alignment requires to take care of this since the periodic box information becomes basically meaningless.

marscher commented 6 years ago

It is even a mistake to calculate with this flag, if the box is not periodic, because this will break assumptions made by the distance/angle calculation algorithm.