Seminars & Lectures
| * TITLE | Accelerated Simulations and Metastable Analyses of Biological Polymers | ||||||
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| * DATE / TIME | 2015-04-23, 16:30pm | ||||||
| * ABSTRACT | |||||||
| Conformational space of complex system such as biological macromolecule is not easy to be ergodic in atomistic molecular dynamics simulations within the usual computational source, and it is also not trivial to analyze the generated simulation data to understand the systems. Ensemble dynamics simulation, which generated independent multiple short trajectories started from different initial conformations, has some advantages in comparison with the single long trajectory simulation. Generalized ensemble simulations, where the normal Boltzmann distribution in conformational space is replaced by another formula, can visit wider range to achieve higher efficient in overcoming free energy barriers. Non-equilibrium simulations also provide a possible way to improve the ability of exploring the conformational regions. We present a methodology to analyze trajectory ensemble of equilibrium and/or non-equilibrium simulations, to identify meta-stable states and to form a kinetic hierarchical transition network among these states for understanding the relation between the microscopic structure of system and its macroscopic behavior. We illustrate the application of the method in liquid-solid phase transition and polypeptides. |
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