کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
10349894 863719 2013 9 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Canonical ensemble simulation of biopolymers using a coarse-grained articulated generalized divide-and-conquer scheme
موضوعات مرتبط
مهندسی و علوم پایه شیمی شیمی تئوریک و عملی
پیش نمایش صفحه اول مقاله
Canonical ensemble simulation of biopolymers using a coarse-grained articulated generalized divide-and-conquer scheme
چکیده انگلیسی
In this paper, a scheme for the canonical ensemble simulation of the coarse-grained articulated polymers is discussed. In this coarse-graining strategy, different subdomains of the system are considered as rigid and/or flexible bodies connected to each other via kinematic joints instead of stiff, but elastic bonds. Herein, the temperature of the simulation is controlled by a Nosé-Hoover thermostat. The dynamics of this feedback control system in the context of multibody dynamics may be represented and solved using traditional methods with computational complexity of O(n3) where n denotes the number of degrees of freedom of the system. In this paper, we extend the divide-and-conquer algorithm (DCA), and apply it to constant temperature molecular simulations. The DCA in its original form uses spatial forces to formulate the equations of motion. The Generalized-DCA applied here properly accommodates the thermostat generalized forces (from the thermostat), which control the temperature of the simulation, in the equations of motion. This algorithm can be implemented in serial and parallel with computational complexity of O(n) and O(logn), respectively.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Computer Physics Communications - Volume 184, Issue 3, March 2013, Pages 652-660
نویسندگان
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