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285
Fast Parallel Algorithms for ShortRange Molecular Dynamics
 JOURNAL OF COMPUTATIONAL PHYSICS
, 1995
"... Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of interatomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dyn ..."
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Cited by 622 (6 self)
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Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of interatomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently  those with shortrange forces where the neighbors of each atom change rapidly. They can be implemented on any distributedmemory parallel machine which allows for messagepassing of data between independently executing processors. The algorithms are tested on a standard LennardJones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers  the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray YMP and C90 algorithm shows that the current generation of parallel machines is competitive with conventi...
The PARSEC benchmark suite: Characterization and architectural implications
 IN PRINCETON UNIVERSITY
, 2008
"... This paper presents and characterizes the Princeton Application Repository for SharedMemory Computers (PARSEC), a benchmark suite for studies of ChipMultiprocessors (CMPs). Previous available benchmarks for multiprocessors have focused on highperformance computing applications and used a limited ..."
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Cited by 486 (3 self)
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This paper presents and characterizes the Princeton Application Repository for SharedMemory Computers (PARSEC), a benchmark suite for studies of ChipMultiprocessors (CMPs). Previous available benchmarks for multiprocessors have focused on highperformance computing applications and used a limited number of synchronization methods. PARSEC includes emerging applications in recognition, mining and synthesis (RMS) as well as systems applications which mimic largescale multithreaded commercial programs. Our characterization shows that the benchmark suite covers a wide spectrum of working sets, locality, data sharing, synchronization and offchip traffic. The benchmark suite has been made available to the public.
NAMD2: Greater Scalability for Parallel Molecular Dynamics
 JOURNAL OF COMPUTATIONAL PHYSICS
, 1998
"... Molecular dynamics programs simulate the behavior of biomolecular systems, leading to insights and understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this ..."
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Cited by 317 (45 self)
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Molecular dynamics programs simulate the behavior of biomolecular systems, leading to insights and understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scalable program. It is also necessary that the program be easily modified by applicationdomain programmers. The
Geometric numerical integration illustrated by the StörmerVerlet method
, 2003
"... The subject of geometric numerical integration deals with numerical integrators that preserve geometric properties of the flow of a differential equation, and it explains how structure preservation leads to improved longtime behaviour. This article illustrates concepts and results of geometric nume ..."
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Cited by 65 (6 self)
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The subject of geometric numerical integration deals with numerical integrators that preserve geometric properties of the flow of a differential equation, and it explains how structure preservation leads to improved longtime behaviour. This article illustrates concepts and results of geometric numerical integration on the important example of the Störmer–Verlet method. It thus presents a crosssection of the recent monograph by the authors, enriched by some additional material. After an introduction to the Newton–Störmer–Verlet–leapfrog method and its various interpretations, there follows a discussion of geometric properties: reversibility, symplecticity, volume preservation, and conservation of first integrals. The extension to Hamiltonian systems on manifolds is also described. The theoretical foundation relies on a backward error analysis, which translates the geometric properties of the method into the structure of a modified differential equation, whose flow is nearly identical to the numerical method. Combined with results from perturbation theory, this explains the excellent longtime behaviour of the method: longtime energy conservation, linear error growth and preservation of invariant tori in nearintegrable systems, a discrete virial theorem, and preservation of adiabatic invariants.
Symplectic Numerical Integrators in Constrained Hamiltonian Systems
, 1994
"... : Recent work reported in the literature suggests that for the longtime integration of Hamiltonian dynamical systems one should use methods that preserve the symplectic (or canonical) structure of the flow. Here we investigate the symplecticness of numerical integrators for constrained dynamics, su ..."
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Cited by 62 (8 self)
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: Recent work reported in the literature suggests that for the longtime integration of Hamiltonian dynamical systems one should use methods that preserve the symplectic (or canonical) structure of the flow. Here we investigate the symplecticness of numerical integrators for constrained dynamics, such as occur in molecular dynamics when bond lengths are made rigid in order to overcome stepsize limitations due to the highest frequencies. This leads to a constrained Hamiltonian system of smaller dimension. Previous work has shown that it is possible to have methods which are symplectic on the constraint manifold in phase space. Here it is shown that the very popular Verlet method with SHAKEtype constraints is equivalent to the same method with RATTLEtype constraints and that the latter is symplectic and time reversible. (This assumes that the iteration is carried to convergence.) We also demonstrate the global convergence of the Verlet scheme in the presence of SHAKEtype and RATTLE...
Advanced character physics
 IN PROCEEDINGS OF THE GAME DEVELOPERS CONFERENCE 2001
, 2001
"... This paper explains the basic elements of an approach to physicallybased modeling which is well suited for interactive use. It is simple, fast, and quite stable, and in its basic version the method does not require knowledge of advanced mathematical subjects (although it is based on a solid mathema ..."
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Cited by 47 (0 self)
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This paper explains the basic elements of an approach to physicallybased modeling which is well suited for interactive use. It is simple, fast, and quite stable, and in its basic version the method does not require knowledge of advanced mathematical subjects (although it is based on a solid mathematical foundation). It allows for simulation of both cloth; soft and rigid bodies; and even articulated or constrained bodies using both forward and inverse kinematics. The algorithms were developed for IO Interactive‟s game Hitman: Codename 47. There, among other things, the physics system was responsible for the movement of cloth, plants, rigid bodies, and for making dead human bodies fall in unique ways depending on where they were hit, fully interacting with the environment (resulting in the press oxymoron “lifelike death animations”). The article also deals with subtleties like penetration test optimization and friction handling. 1
THEORETICAL AND NUMERICAL COMPARISON OF SOME SAMPLING METHODS FOR MOLECULAR DYNAMICS
, 2005
"... The purpose of the present article is to compare different phasespace sampling methods, such as purely stochastic methods (Rejection method, Metropolized independence sampler, Importance Sampling), stochastically perturbed Molecular Dynamics (Hybrid Monte Carlo, Langevin Dynamics, Biased Random Wal ..."
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Cited by 39 (3 self)
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The purpose of the present article is to compare different phasespace sampling methods, such as purely stochastic methods (Rejection method, Metropolized independence sampler, Importance Sampling), stochastically perturbed Molecular Dynamics (Hybrid Monte Carlo, Langevin Dynamics, Biased Random Walk), and purely deterministic methods (NoséHoover chains, NoséPoincaré and Recursive Multiple Thermostats (RMT) methods). After recalling some theoretical convergence properties for the various methods, we provide some new convergence results for the Hybrid Monte Carlo scheme, requiring weaker (and easier to check) conditions than previously known conditions. We then turn to the numerical efficiency of the sampling schemes for a benchmark model of linear alkane molecules. In particular, the numerical distributions that are generated are compared in a systematic way, on the basis of some quantitative convergence indicators.
Algorithmic challenges in computational molecular biophysics
 Journal of Computational Physics
, 1999
"... A perspective of biomolecular simulations today is given, with illustrative applications and an emphasis on algorithmic challenges, as reflected by the work of a multidisciplinary team of investigators from five institutions. Included are overviews and recent descriptions of algorithmic work in long ..."
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Cited by 37 (3 self)
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A perspective of biomolecular simulations today is given, with illustrative applications and an emphasis on algorithmic challenges, as reflected by the work of a multidisciplinary team of investigators from five institutions. Included are overviews and recent descriptions of algorithmic work in longtime integration for molecular dynamics; fast electrostatic evaluation; crystallographic refinement approaches; and implementation of large, computationintensive programs on modern architectures. Expected future developments of the field are also discussed. c ○ 1999 Academic Press Key Words: biomolecular simulations; molecular dynamics; longtime integration; fast electrostatics; crystallographic refinement; highperformance platforms.
Geometric Integrators for ODEs
 J. Phys. A
, 2006
"... Abstract. Geometric integration is the numerical integration of a differential equation, while preserving one or more of its “geometric ” properties exactly, i.e. to within roundoff error. Many of these geometric properties are of crucial importance in physical applications: preservation of energy, ..."
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Cited by 36 (6 self)
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Abstract. Geometric integration is the numerical integration of a differential equation, while preserving one or more of its “geometric ” properties exactly, i.e. to within roundoff error. Many of these geometric properties are of crucial importance in physical applications: preservation of energy, momentum, angular momentum, phase space volume, symmetries, timereversal symmetry, symplectic structure and dissipation are examples. In this paper we present a survey of geometric numerical integration methods for ordinary differential equations. Our aim has been to make the review of use for both the novice and the more experienced practitioner interested in the new developments and directions of the past decade. To this end, the reader who is interested in reading up on detailed technicalities will be provided with numerous signposts to the relevant literature. Geometric Integrators for ODEs 2 1.
Tryptophan fluorescence shifts in proteins from hybrid simulations: an electrostatic approach
, 1997
"... ABSTRACT Tryptophan fluorescence wavelength is widely used as a tool to monitor changes in proteins and to make inferences regarding local structure and dynamics. We have predicted the fluorescence wavelengths of 19 tryptophans in 16 proteins, starting with crystal structures and using a hybrid quan ..."
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Cited by 35 (1 self)
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ABSTRACT Tryptophan fluorescence wavelength is widely used as a tool to monitor changes in proteins and to make inferences regarding local structure and dynamics. We have predicted the fluorescence wavelengths of 19 tryptophans in 16 proteins, starting with crystal structures and using a hybrid quantum mechanicalclassical molecular dynamics method with the assumption that only electrostatic interactions of the tryptophan ring electron density with the surrounding protein and solvent affect the transition energy. With only one adjustable parameter, the scaling of the quantum mechanical atomic charges as seen by the protein/solvent environment, the mean absolute deviation between predicted and observed fluorescence maximum wavelength is 6 nm. The modeling of electrostatic interactions, including hydration, in proteins is vital to understanding function and structure, and this study helps to assess the effectiveness of current electrostatic models.