کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
1959069 1057926 2006 9 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Ensemble-Based Convergence Analysis of Biomolecular Trajectories
موضوعات مرتبط
علوم زیستی و بیوفناوری بیوشیمی، ژنتیک و زیست شناسی مولکولی زیست شیمی
پیش نمایش صفحه اول مقاله
Ensemble-Based Convergence Analysis of Biomolecular Trajectories
چکیده انگلیسی

Assessing the convergence of a biomolecular simulation is an essential part of any careful computational investigation, because many fundamental aspects of molecular behavior depend on the relative populations of different conformers. Here we present a physically intuitive method to self-consistently assess the convergence of trajectories generated by molecular dynamics and related methods. Our approach reports directly and systematically on the structural diversity of a simulation trajectory. Straightforward clustering and classification steps are the key ingredients, allowing the approach to be trivially applied to systems of any size. Our initial study on met-enkephalin strongly suggests that even fairly long trajectories (∼50 ns) may not be converged for this small—but highly flexible—system.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: - Volume 91, Issue 1, 1 July 2006, Pages 164–172
نویسندگان
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