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Abstract: this paper, we evaluate the design of ProtoMol [7], a framework for MD that uses encapsulation and generic programming to provide an extensible component platform for parallel algorithms for MD. The emphasis on design and extensibility distinguishes ProtoMol from other excellent MD programs, such as GROMOS [15], Amber [18], CHARMM [2]. A program with similar goals, which provided the initial inspiration for ProtoMol, is NAMD2 [8]. However, NAMD 2's design goal is primarily high scalability,... (Update)
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BibTeX entry: (Update)
Matthey, T., Izaguirre, J.A.: ProtoMol: A molecular dynamics framework with incremental parallelization. In: Proc. of the Tenth SIAM Conf. on Parallel Processing for Scientific Computing (PP01). Proceedings in Applied Mathematics, Philadelphia, Society for Industrial and Applied Mathematics (2001) http://citeseer.ist.psu.edu/article/matthey00protomol.html More
@misc{ matthey01protomol,
author = "T. Matthey and J. Izaguirre",
title = "ProtoMol: A molecular dynamics framework with incremental parallelization",
text = "Matthey, T., Izaguirre, J.A.: ProtoMol: A molecular dynamics framework
with incremental parallelization. In: Proc. of the Tenth SIAM Conf. on Parallel
Processing for Scientific Computing (PP01). Proceedings in Applied Mathematics,
Philadelphia, Society for Industrial and Applied Mathematics (2001)",
year = "2001",
url = "citeseer.ist.psu.edu/article/matthey00protomol.html" }
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25 NAMD2: Greater scalability for parallel molecular dynamics - Kal, Skeel et al. - 1999
9 A domain decomposition parallel processing algorithm for mol.. - Brown, Minoux et al. - 1997
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