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. / A Thesis Submitted to the School of Computational Science in Partial FulfiLlment of
the Requirements for the Degree of Master of Science. / Summer Semester, 2008. / June 20, 2008. / Essential Energy Space Random Walk, Metadynamics Simulations, Wang-Landau Method / Includes bibliographical references. / Wei Yang, Professor Directing Thesis; Gordon Erlebacher, Committee Member; Janet Peterson, Committee Member.
| Identifer | oai:union.ndltd.org:fsu.edu/oai:fsu.digital.flvc.org:fsu_175720 |
| Contributors | Liu, Yusong (authoraut), Yang, Wei (professor directing thesis), Erlebacher, Gordon (committee member), Peterson, Janet (committee member), Department of Scientific Computing (degree granting department), Florida State University (degree granting institution) |
| Publisher | Florida State University, Florida State University |
| Source Sets | Florida State University |
| Language | English, English |
| Detected Language | English |
| Type | Text, text |
| Format | 1 online resource, computer, application/pdf |
| Rights | This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s). The copyright in theses and dissertations completed at Florida State University is held by the students who author them. |
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