科研之友
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摘要
Force field based energy minimization of molecular structures is a central task in computational chemistry and biology. Solving this problem usually requires efficient local minimization techniques, i.e., iterative two-step methods that search first for a descent direction and then try to estimate the step width. The second step, the so called line search, typically uses polynomial interpolation schemes to estimate the next trial step. However, dependent on local properties of the objective function alternative schemes may be more appropriate especially if the objective function shows singularities or exponential behavior. As the choice of the best interpolation scheme cannot be made a priori, we propose a new consensus line search approach that performs several different interpolation schemes at each step and then decides which one is the most reliable at the current position. Although a naive consensus approach Would lead to severe performance impacts, our method does not require additional evaluations of the energy function, imposing only negligible computational overhead. Additionally, our method can be easily adapted to the local behavior of other objective functions by incorporating suitable interpolation schemes or omitting non-fitting schemes. The performance of our consensus line search approach has been evaluated and compared to established standard line search algorithms by minimizing the structures of a large set of molecules using different force fields. The proposed algorithm shows better performance in almost all test cases, i.e., it reduces the number of iterations and function and gradient evaluations, leading to significantly reduced run times.
- 出版日期2009-7-15
- 单位上海生物信息技术研究中心
