Computer simulation of liquids
Computer simulation of liquids
50 GFlops molecular dynamics on the Connection Machine 5
Proceedings of the 1993 ACM/IEEE conference on Supercomputing
Tcl and the Tk toolkit
Message-passing multi-cell molecular dynamics on the Connection Machine 5
Parallel Computing
Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
Exploratory visualization I: real-time interaction
Computers in Physics
SCIRun: a scientific programming environment for computational steering
Supercomputing '95 Proceedings of the 1995 ACM/IEEE conference on Supercomputing
Computers in Physics
Avalon: an Alpha/Linux cluster achieves 10 Gflops for $15k
SC '98 Proceedings of the 1998 ACM/IEEE conference on Supercomputing
An Extensible Compiler for Creating Scriptable Scientific Software
ICCS '02 Proceedings of the International Conference on Computational Science-Part II
Extensible Message Passing Application Development and Debugging with Python
IPPS '97 Proceedings of the 11th International Symposium on Parallel Processing
Automated scientific software scripting with SWIG
Future Generation Computer Systems - Tools for program development and analysis
Engineering high-performance legacy codes as CORBA components for problem-solving environments
Journal of Parallel and Distributed Computing
SGrid: a service-oriented model for the Semantic grid
Future Generation Computer Systems - Special issue: Semantic grid and knowledge grid: the next-generation web
ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics
ACM Transactions on Mathematical Software (TOMS)
Leveraging legacy codes to distributed problem-solving environments: a web services approach
Software—Practice & Experience
An Object-Oriented Design for Two-Dimensional Vortex Particle Methods
ACM Transactions on Mathematical Software (TOMS)
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Environmental Modelling & Software
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We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.