کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
522148 867812 2007 16 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Using the method of weighted residuals to compute potentials of mean force
موضوعات مرتبط
مهندسی و علوم پایه مهندسی کامپیوتر نرم افزارهای علوم کامپیوتر
پیش نمایش صفحه اول مقاله
Using the method of weighted residuals to compute potentials of mean force
چکیده انگلیسی

We propose a general framework for approximating the potential of mean force (PMF) along a reaction coordinate in conformational space. This framework, based on the method of weighted residuals, can be viewed as a generalization of thermodynamic integration and direct histogram methods. Using weighted residuals allows for higher-order approximations to the PMF in the form of a global spectral method or a finite element method. In addition, the higher degree of continuity provided by spectral and higher-order elements makes weighted residual methods an attractive choice for use in tandem with biasing force methods. As an analysis tool, the weighted residuals framework provides a context for direct comparison of thermodynamic integration and histogram based methods. For validation of the new method, numerical experiments are performed on two systems: a simple double-well and alanine dipeptide in vacuum. Comparisons between the new weighted residual methods, thermodynamic integration, and WHAM are performed. When configuration space is perfectly sampled the high-order weighted residual methods are found to exhibit exponential convergence. For more realistic sampling, the weighted residual methods performed comparably to the other two. However, results suggest that spectral type methods are more robust with respect to parameter choices describing the solution space.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Computational Physics - Volume 225, Issue 1, 1 July 2007, Pages 714–729
نویسندگان
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