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 AbstractMetadynamics 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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