TY - JOUR

T1 - Canonical ensemble simulation of biopolymers using a coarse-grained articulated generalized divide-And-conquer scheme

AU - Poursina, Mohammad

AU - Anderson, Kurt S.

N1 - Funding Information:
Support for this work received under the National Science Foundation through award no. 0757936 is gratefully acknowledged. The authors would like to thank Mr. Michael Sherman from the Simbios National Institute of Health Research Center for biomedical simulations at Stanford University for the discussions they have had with him. The simulations in the GDCA scheme have been performed by modifying the DCA code developed by Dr. Kishor Bhalerao in his Ph.D. dissertation [59] .

PY - 2013/3

Y1 - 2013/3

N2 - 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.

AB - 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.

KW - Canonical ensemble

KW - Coarse-grained modeling

KW - Generalized divide-And-conquer-Algorithm

KW - Multibody dynamics

KW - Nosé-Hoover thermostat

KW - Thermostat generalized feedback force

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U2 - 10.1016/j.cpc.2012.10.029

DO - 10.1016/j.cpc.2012.10.029

M3 - Article

AN - SCOPUS:84872024893

VL - 184

SP - 652

EP - 660

JO - Computer Physics Communications

JF - Computer Physics Communications

SN - 0010-4655

IS - 3

ER -