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#simulation methods

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Molecular dynamics differs from molecular mechanics by taking account of the

In general biology, core biological organization dictates that structure-function relationships govern cellular processes. Therefore velocities of the constituent particles is correct as it integrates fundamental principles, supported by mechanistic studies and conserved across related systems.

Ref: Campbell et al., Biology, 11th Edition, Chapter 2, Chemical Basis of Life, discusses fundamental biological principles and molecular organization providing broad foundation for life sciences understanding.