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Results 1 - 10
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657
Scalable molecular dynamics with NAMD.
- J Comput Chem
, 2005
"... Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and la ..."
Abstract
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Cited by 849 (63 self)
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Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop
On the parallelization of molecular dynamics codes
, 2002
"... Abstract Molecular dynamics (MD) codes present a high degree of spatial data locality and a significant amount of independent computations. However, most of the parallelization strategies are usually based on the manual transformation of sequential programs either by completely rewriting the code w ..."
Abstract
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Abstract Molecular dynamics (MD) codes present a high degree of spatial data locality and a significant amount of independent computations. However, most of the parallelization strategies are usually based on the manual transformation of sequential programs either by completely rewriting the code
Communication Optimizations for Irregular Scientific Computations on Distributed Memory Architectures
- Journal of Parallel and Distributed Computing
, 1993
"... This paper describes a number of optimizations that can be used to support the efficient execution of irregular problems on distributed memory parallel machines. These primitives (1) coordinate interprocessor data movement, (2) manage the storage of, and access to, copies of off-processor data, (3) ..."
Abstract
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Cited by 144 (17 self)
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unstructured adaptive application (the molecular dynamics code CHARMM). 1 Introduction Over the past few years we have developed a methodology to produce efficient distributed memory code for sparse and unstructured problems in which array accesses are made through a level of indirection. In such problems
Scalable algorithms for molecular dynamics simulations on commodity clusters
- In SC ’06: Proceedings of the 2006 ACM/IEEE Conference on Supercomputing
, 2006
"... Although molecular dynamics (MD) simulations of biomolecular systems often run for days to months, many events of great scientific interest and pharmaceutical relevance occur on long time scales that remain beyond reach. We present several new algorithms and implementation techniques that significan ..."
Abstract
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Cited by 68 (5 self)
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Although molecular dynamics (MD) simulations of biomolecular systems often run for days to months, many events of great scientific interest and pharmaceutical relevance occur on long time scales that remain beyond reach. We present several new algorithms and implementation techniques
GFlops Molecular Dynamics on the Connection Machine 5
- In Proceedings of Supercomputing 93 (IEEE Computer Society Press, Los Alamitos, CA
, 1993
"... We present timings and performance numbers for a new short range three dimensional (3D) molecular dynamics (MD) code, SPaSM, on the Connection Machine-5 (CM-5). We demonstrate that runs with more than 10 8 particles are now possible on massively parallel MIMD computers. To the best of our knowledg ..."
Abstract
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Cited by 10 (3 self)
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We present timings and performance numbers for a new short range three dimensional (3D) molecular dynamics (MD) code, SPaSM, on the Connection Machine-5 (CM-5). We demonstrate that runs with more than 10 8 particles are now possible on massively parallel MIMD computers. To the best of our
Large-Scale Molecular-Dynamics Simulation of 19 Billion Particles
- Int. J. Modern Phys. C
, 2004
"... We have performed parallel large-scale molecular-dynamics simulations on the QSCmachine at Los Alamos. The good scalability of the SPaSM code is demonstrated together with its capability of efficient data analysis for enormous system sizes up to 19 000 416 964 particles. Furthermore, we introduce a ..."
Abstract
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Cited by 10 (1 self)
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We have performed parallel large-scale molecular-dynamics simulations on the QSCmachine at Los Alamos. The good scalability of the SPaSM code is demonstrated together with its capability of efficient data analysis for enormous system sizes up to 19 000 416 964 particles. Furthermore, we introduce a
Las palmeras molecular dynamics: a flexible and modular molecular dynamics code
- Comput. Phys. Commun
"... Las Palmeras Molecular Dynamics (LPMD) is a Molecular Dynamics (MD) code written from scratch in C++, as user-friendly, modular and multiplatform as possible. Some of its features are: it is an Open Source code, it works using plugins, it reads simple and intuitive configuration files, and includes ..."
Abstract
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Cited by 2 (1 self)
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Las Palmeras Molecular Dynamics (LPMD) is a Molecular Dynamics (MD) code written from scratch in C++, as user-friendly, modular and multiplatform as possible. Some of its features are: it is an Open Source code, it works using plugins, it reads simple and intuitive configuration files, and includes
NAMD: biomolecular simulation on thousands of processors
- In Supercomputing
, 2002
"... Abstract NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoff electrostatics on up to 2048 processors of the ASCI Red machine, achieved with ..."
Abstract
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Cited by 113 (33 self)
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Abstract NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoff electrostatics on up to 2048 processors of the ASCI Red machine, achieved
COMPILED HARDWARE ACCELERATION OF MOLECULAR DYNAMICS CODE
"... The objective of Molecular Dynamics (MD) simulations is to determine the shape of a molecule in a given biomolecular environment. These simulations are very demanding computationally, where simulations of a few milliseconds can take days or months depending on the number of atoms involved. Therefore ..."
Abstract
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Cited by 3 (2 self)
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The objective of Molecular Dynamics (MD) simulations is to determine the shape of a molecule in a given biomolecular environment. These simulations are very demanding computationally, where simulations of a few milliseconds can take days or months depending on the number of atoms involved
Molecular dynamics
"... met cons s, a dify al o ter SEA predicted monomer barrier is the same as DFT, while experimental barriers for monomers and dimers are ion dy ng het ts [1–4 eous s eous sy is stud (EAM) is well suited for metallic systems combining pair interac-tions with an atomic embedding energy term dependent on ..."
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the surface VASP [18,19] a density-functional code using a plane-wave basis and ultrasoft Vanderbilt-type pseudopotentials [20,21]. The local-density approximation as parameterized by Perdew and Zunger [22] and a plane-wave kinetic-energy cut-off of 200 eV ensures accurate treatment of the Cu and Ag potential
Results 1 - 10
of
657
