![]() With respect to protein dynamics, local motions, such as bond stretching, occur within femtoseconds, while rigid body and large-scale motions, occur within a range of nanoseconds to seconds. ![]() ![]() Molecular dynamics (MD) simulation is a computational tool used to study molecular systems as they evolve through time. ![]() In this dissertation, we develop a method for molecular simulation based on principal component analysis (PCA) of a molecular dynamics trajectory and least squares approximation of a potential energy function. A reduced basis method for molecular dynamics simulation
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