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General to consider
Mateusz Bieniek edited this page Nov 30, 2020
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Checks of the overall design and possible bugs:
- fixme - you should check if you can rely on atomName and hash for uniqueness which you need
- fixme - make sure that the "bonds" are obeyed, if an atom changes its biding, e.g. it has a double bond and then it has one more hydrogen, then that is a very different atom, and both need to correctly evolve into each other. Note however that when making and ambertop input file for the MD, the bonds are ignored anyway. For that reason we started ignoring the bonds in the checks (see issues).
- Consider thinking about rotatable bonds and how to account for them