Type of Document	Thesis
Author	Liu, Yusong
URN	etd-07142008-134638
Title	Improvement in Metadynamics Simulations: the Essential Energy Space Random Walk and the Wang-Landau Recursion
Degree	Master of Science
Department	Scientific Computing, Department of
Advisory Committee	Advisor Name Title Wei Yang Committee Chair Gordon Erlebacher Committee Member Janet Peterson Committee Member
Keywords	Essential Energy Space Random Walk Metadynamics Simulations Wang-Landau Method
Date of Defense	2008-06-20
Availability	unrestricted
Abstract Metadynamics is a popular tool to explore free energy landscapes and it has been used 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.
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