Canonical ensemble simulation of biopolymers using a coarse-grained articulated generalized divide-And-conquer scheme

Mohammad Poursina, Kurt S. Anderson

Research output: Contribution to journalArticle

18 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)652-660
Number of pages9
JournalComputer Physics Communications
Volume184
Issue number3
DOIs
StatePublished - Mar 1 2013

Keywords

  • Canonical ensemble
  • Coarse-grained modeling
  • Generalized divide-And-conquer-Algorithm
  • Multibody dynamics
  • Nosé-Hoover thermostat
  • Thermostat generalized feedback force

ASJC Scopus subject areas

  • Hardware and Architecture
  • Physics and Astronomy(all)

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