Computer simulation of liquids
Computer simulation of liquids
NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
Scalable algorithms for molecular dynamics simulations on commodity clusters
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Simulating the Physical World: Hierarchical Modeling from Quantum Mechanics to Fluid Dynamics
Simulating the Physical World: Hierarchical Modeling from Quantum Mechanics to Fluid Dynamics
Entering the petaflop era: the architecture and performance of Roadrunner
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
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In many molecular dynamics simulation software packages and hardware implementations, piecewise polynomials are used to represent and compute pairwise potential functions efficiently. In this paper, we present three modifications applicable to most interpolations to increase their accuracy. The increased accuracy reduces the amount of data that needs to be stored for each interaction potential, making such interpolations more suitable for architectures with limited memory and/or cache or hardware implementations.