Quantum mechanical free energy calculations using path integral molecular dynamics
Abstract
Free energy calculations are one of the most powerful tools within modern theoretical chemistry and are often used to make comparisons with experimental results. Existing free energy calculations are typically performed for classical molecular dynamics simulations but there are certain systems where nuclear quantum effects play an integral role. Specifically, systems with light atoms or low temperatures are the most influenced by such nuclear quantum effects and the development of Feynman path integrals [1] has been effective in accurately describing the quantum nature of these nuclei [2–8]. The primary objective of this thesis is the development of a pair of methodologies to calculate free energies utilizing path integral molecular dynamics to account for nuclear quantum effects. \n \n \nPrior to the development of these free energy methodologies, this thesis presents a communication interface between the OpenMM and MMTK software packages that has been previously published [9]. This interface allows for users of MMTK to take advantage of the performance of OpenMM without major modifications to existing simulation scripts. Notably, the serial OpenMM integrator is shown to provide a 3x performance gain in comparison to a standard MMTK simulation while the GPU implementations of OpenMM provide over a 400x performance gain for larger systems with periodic boundary conditions. \n \nThe first path integral free energy methodology of this thesis combines the existing um- brella…
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