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Frequently Asked Questions
Riccardo Alessandri edited this page Dec 14, 2023
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Which atom numbering does PySAGES use?
Zero-based numbering. This means that the first atom in your system will be referred to with index 0 in the CV definition.
For example, a dihedral angle between the 5th, 7th, 9th, and 15th atoms of a system will be defined as:
cvs = [DihedralAngle((4, 6, 8, 14))]