Fast parallel algorithms for short-range molecular dynamics
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TLDR
In this article, three parallel algorithms for classical molecular dynamics are presented, which can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors.About:
This article is published in Journal of Computational Physics.The article was published on 1995-03-01 and is currently open access. It has received 32670 citations till now. The article focuses on the topics: Intel Paragon & Intel iPSC.read more
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GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
Mark Abraham,Teemu Murtola,Roland Schulz,Roland Schulz,Szilárd Páll,Jeremy C. Smith,Jeremy C. Smith,Berk Hess,Erik Lindahl,Erik Lindahl +9 more
TL;DR: GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules, and provides a rich set of calculation types.
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Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool
TL;DR: The Open Visualization Tool (OVITO) as discussed by the authors is a 3D visualization software designed for post-processing atomistic data obtained from molecular dynamics or Monte Carlo simulations, which is written in object-oriented C++, controllable via Python scripts and easily extendable through a plug-in interface.
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Advanced capabilities for materials modelling with Quantum ESPRESSO.
Paolo Giannozzi,Oliviero Andreussi,Oliviero Andreussi,Thomas Brumme,Oana Bunau,M. Buongiorno Nardelli,Matteo Calandra,Roberto Car,Carlo Cavazzoni,Davide Ceresoli,Matteo Cococcioni,Nicola Colonna,Ivan Carnimeo,A. Dal Corso,S. de Gironcoli,Pietro Delugas,Robert A. DiStasio,Andrea Ferretti,Andrea Floris,Guido Fratesi,Giorgia Fugallo,Ralph Gebauer,Uwe Gerstmann,Feliciano Giustino,Tommaso Gorni,Tommaso Gorni,Junteng Jia,Mitsuaki Kawamura,Hsin-Yu Ko,Anton Kokalj,Emine Kucukbenli,Michele Lazzeri,M. Marsili,Nicola Marzari,Francesco Mauri,Ngoc Linh Nguyen,Huy-Viet Nguyen,Alberto Otero-de-la-Roza,Lorenzo Paulatto,Samuel Poncé,Dario Rocca,Dario Rocca,Riccardo Sabatini,Biswajit Santra,Martin Schlipf,Ari P. Seitsonen,Ari P. Seitsonen,Alexander Smogunov,Iurii Timrov,Timo Thonhauser,Paolo Umari,Nathalie Vast,Xifan Wu,Stefano Baroni +53 more
TL;DR: Recent extensions and improvements are described, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.
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Changes in portlandite morphology with solvent composition: Atomistic simulations and experiment
TL;DR: In this article, a new analysis tool was developed to quantify the experimentally observed changes in morphology of portlandite, allowing the calculation of the relative surface energies of the crystal facets.
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Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.
TL;DR: An implementation of explicit solvent all atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA-enabled GPUs, providing results that are statistically indistinguishable from the traditional CPU version of the software and with performance that exceeds that achievable by the CPUs running on all conventional CPU-based clusters and supercomputers.
References
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Michael P. Allen,D. J. Tildesley +1 more
TL;DR: In this paper, the gear predictor -corrector is used to calculate forces and torques in a non-equilibrium molecular dynamics simulation using Monte Carlo methods. But it is not suitable for the gear prediction problem.
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TL;DR: In this paper, a simulation program for particle-mesh force calculation is presented, based on a one-dimensional plasma model and a collisionless particle model, which is used to simulate collisionless particle models.
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Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals
Murray S. Daw,Michael I. Baskes +1 more
TL;DR: In this paper, the authors derived an expression for the total energy of a metal using the embedding energy from which they obtained several ground-state properties, such as the lattice constant, elastic constants, sublimation energy, and vacancy-formation energy.
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A fast algorithm for particle simulations
TL;DR: An algorithm is presented for the rapid evaluation of the potential and force fields in systems involving large numbers of particles whose interactions are Coulombic or gravitational in nature, making it considerably more practical for large-scale problems encountered in plasma physics, fluid dynamics, molecular dynamics, and celestial mechanics.