Error analysis of the poisson P 3M force field scheme for particle-based simulations of biological systems

David Marreiro; Shela Aboud; Marco Saraniti; Robert Eisenberg

Error analysis of the poisson P ³M force field scheme for particle-based simulations of biological systems

David Marreiro, Shela Aboud, Marco Saraniti, Robert Eisenberg

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

The analysis of the errors associate with the real space Poisson particle-particle-particle-mesh (P ³M) force field approach for biological systems is presented. The methods to improve the efficiency and accuracy of the P ³M are also discussed. The P ³M approach accounts for both long-lange and short-range electrostatic interactions in the simulation of biological systems. For the accuracy assessment of the approach, the radial distribution function (RDF) of the ionic population is calculated with Brownian dynamics, and compared with the analytic solution of the Ornstein-Zernike equation, using the hypernetted-chain closure relation.

Original language	English (US)
Title of host publication	2004 10th International Workshop on Computational Electronics, IEEE IWCE-10 2004, Abstracts
Pages	203-204
Number of pages	2
State	Published - Dec 1 2004
Externally published	Yes
Event	2004 10th International Workshop on Computational Electronics: The Field of Computational Electronics - Looking Back and Looking Ahead, IEEE IWCE-10 2004, Abstracts - West Lafayette, IN, United States Duration: Oct 24 2004 → Oct 27 2004

Publication series

Name	2004 10th International Workshop on Computational Electronics, IEEE IWCE-10 2004, Abstracts

Other

Other	2004 10th International Workshop on Computational Electronics: The Field of Computational Electronics - Looking Back and Looking Ahead, IEEE IWCE-10 2004, Abstracts
Country/Territory	United States
City	West Lafayette, IN
Period	10/24/04 → 10/27/04

ASJC Scopus subject areas

Engineering(all)

Cite this

Marreiro, D., Aboud, S., Saraniti, M., & Eisenberg, R. (2004). Error analysis of the poisson P ³M force field scheme for particle-based simulations of biological systems. In 2004 10th International Workshop on Computational Electronics, IEEE IWCE-10 2004, Abstracts (pp. 203-204). (2004 10th International Workshop on Computational Electronics, IEEE IWCE-10 2004, Abstracts).

Error analysis of the poisson P ³M force field scheme for particle-based simulations of biological systems. / Marreiro, David; Aboud, Shela; Saraniti, Marco et al.
2004 10th International Workshop on Computational Electronics, IEEE IWCE-10 2004, Abstracts. 2004. p. 203-204 (2004 10th International Workshop on Computational Electronics, IEEE IWCE-10 2004, Abstracts).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Marreiro, D, Aboud, S, Saraniti, M & Eisenberg, R 2004, Error analysis of the poisson P ³M force field scheme for particle-based simulations of biological systems. in 2004 10th International Workshop on Computational Electronics, IEEE IWCE-10 2004, Abstracts. 2004 10th International Workshop on Computational Electronics, IEEE IWCE-10 2004, Abstracts, pp. 203-204, 2004 10th International Workshop on Computational Electronics: The Field of Computational Electronics - Looking Back and Looking Ahead, IEEE IWCE-10 2004, Abstracts, West Lafayette, IN, United States, 10/24/04.

Marreiro, David ; Aboud, Shela ; Saraniti, Marco et al. / Error analysis of the poisson P ³M force field scheme for particle-based simulations of biological systems. 2004 10th International Workshop on Computational Electronics, IEEE IWCE-10 2004, Abstracts. 2004. pp. 203-204 (2004 10th International Workshop on Computational Electronics, IEEE IWCE-10 2004, Abstracts).

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abstract = "The analysis of the errors associate with the real space Poisson particle-particle-particle-mesh (P 3M) force field approach for biological systems is presented. The methods to improve the efficiency and accuracy of the P 3M are also discussed. The P 3M approach accounts for both long-lange and short-range electrostatic interactions in the simulation of biological systems. For the accuracy assessment of the approach, the radial distribution function (RDF) of the ionic population is calculated with Brownian dynamics, and compared with the analytic solution of the Ornstein-Zernike equation, using the hypernetted-chain closure relation.",

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