Title:
EWALD SUMMATION METHOD FOR MOLECULAR SIMULATION
Document Type and Number:
WIPO Patent Application WO2006004877
Kind Code:
A3
Abstract:
The invention includes a method and associated software and a system in which bodies are spatially partitioned among computational nodes and wherein each computational node maintains data for a different subset of the bodies. The method includes, importing body data from a set of one of more spatially neighbor nodes and, computing data characterizing interactions between bodies.
Inventors:
SHAW DAVID E (US)
SHAN YIBING (US)
KLEPEIS JOHN (US)
EASTWOOD MICHAEL (US)
DROR RON (US)
SHAN YIBING (US)
KLEPEIS JOHN (US)
EASTWOOD MICHAEL (US)
DROR RON (US)
Application Number:
PCT/US2005/023184
Publication Date:
February 09, 2006
Filing Date:
June 30, 2005
Export Citation:
Assignee:
D E SHAW RES AND DEV LLC (US)
SHAW DAVID E (US)
SHAN YIBING (US)
KLEPEIS JOHN (US)
EASTWOOD MICHAEL (US)
DROR RON (US)
SHAW DAVID E (US)
SHAN YIBING (US)
KLEPEIS JOHN (US)
EASTWOOD MICHAEL (US)
DROR RON (US)
International Classes:
G06F17/50; G16B15/00
Other References:
TOUKMAJI A Y ET AL: "Ewald summation techniques in perspective: a survey", COMPUTER PHYSICS COMMUNICATIONS ELSEVIER NETHERLANDS, vol. 95, no. 2-3, June 1996 (1996-06-01), pages 73 - 92, XP002358596, ISSN: 0010-4655
LEONID Y. ZASLAVSKY, TAMAR SCHLICK: "An adaptive multigrid technique for evaluating long-range forces in biomolecular simulations", APPLIED MATHEMATICS AND COMPUTATION, vol. 97, no. 2-3, 15 December 1998 (1998-12-15), pages 237 - 250, XP002358597
DEHNEN W: "A hierarchical O(N) force calculation algorithm", JOURNAL OF COMPUTATIONAL PHYSICS ACADEMIC PRESS USA, vol. 179, no. 1, 10 June 2002 (2002-06-10), pages 27 - 42, XP002358598, ISSN: 0021-9991
DARDEN T ET AL: "New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations.", STRUCTURE WITH FOLDING & DESIGN. 15 MAR 1999, vol. 7, no. 3, 15 March 1999 (1999-03-15), pages R55 - R60, XP002358599, ISSN: 0969-2126
SCHLICK T ET AL: "Algorithmic challenges in computational molecular biophysics", JOURNAL OF COMPUTATIONAL PHYSICS ACADEMIC PRESS USA, vol. 151, no. 1, 1 May 1999 (1999-05-01), pages 9 - 48, XP002358600, ISSN: 0021-9991
SAGUI C ET AL: "Molecular dynamics simulations of biomolecules: long-range electrostatic effects.", ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE. 1999, vol. 28, 1999, pages 155 - 179, XP002358601, ISSN: 1056-8700
GREENGARD L F ET AL: "A new version of the fast multipole method for screened Coulomb interactions in three dimensions", JOURNAL OF COMPUTATIONAL PHYSICS ACADEMIC PRESS USA, vol. 180, no. 2, 10 August 2002 (2002-08-10), pages 642 - 658, XP002358602, ISSN: 0021-9991
LEONID Y. ZASLAVSKY, TAMAR SCHLICK: "An adaptive multigrid technique for evaluating long-range forces in biomolecular simulations", APPLIED MATHEMATICS AND COMPUTATION, vol. 97, no. 2-3, 15 December 1998 (1998-12-15), pages 237 - 250, XP002358597
DEHNEN W: "A hierarchical O(N) force calculation algorithm", JOURNAL OF COMPUTATIONAL PHYSICS ACADEMIC PRESS USA, vol. 179, no. 1, 10 June 2002 (2002-06-10), pages 27 - 42, XP002358598, ISSN: 0021-9991
DARDEN T ET AL: "New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations.", STRUCTURE WITH FOLDING & DESIGN. 15 MAR 1999, vol. 7, no. 3, 15 March 1999 (1999-03-15), pages R55 - R60, XP002358599, ISSN: 0969-2126
SCHLICK T ET AL: "Algorithmic challenges in computational molecular biophysics", JOURNAL OF COMPUTATIONAL PHYSICS ACADEMIC PRESS USA, vol. 151, no. 1, 1 May 1999 (1999-05-01), pages 9 - 48, XP002358600, ISSN: 0021-9991
SAGUI C ET AL: "Molecular dynamics simulations of biomolecules: long-range electrostatic effects.", ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE. 1999, vol. 28, 1999, pages 155 - 179, XP002358601, ISSN: 1056-8700
GREENGARD L F ET AL: "A new version of the fast multipole method for screened Coulomb interactions in three dimensions", JOURNAL OF COMPUTATIONAL PHYSICS ACADEMIC PRESS USA, vol. 180, no. 2, 10 August 2002 (2002-08-10), pages 642 - 658, XP002358602, ISSN: 0021-9991
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