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Metadynamics is a popular tool to explore free energy landscapes and it has been use to elucidate various chemical or biochemical processes. The height of updating Gaussian function is very important for proper free energy convergence to the target free energy surface. Both higher and lower Gaussian heights have advantages and disadvantages, a balance is required. This thesis presents the implementation of the Wang-Landau recursion scheme in metadynamics simulations to adjust the height of the unit Gaussian function. Compared with classical fixed Gaussian heights, this dynamic adjustable method was demonstrated to efficiently yield better converged free energy surfaces. In addition, through combination with the realization of an energy space random walk, the Wang-Landau recursion scheme can be readily used to deal with the pseudoergodicity problem in molecular dynamic simulations. The use of this scheme is proven to efficiently and robustly obtain a biased free energy function within this thesis.
Essential Energy Space Random Walk, Metadynamics Simulations, Wang-Landau Method
Date of Defense
June 20, 2008.
A Thesis Submitted to the School of Computational Science in Partial FulﬁLlment of the Requirements for the Degree of Master of Science.
Includes bibliographical references.
Florida State University
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