J. A. Izaguirre, J. Willcock, T. Matthey, T. B. Slabach, T. Steinbach, S. Stender, G. F. Viamontes, and J. Mohnke. ProtoMol: An object oriented framework for molecular dynamics. http://www.cse.nd.edu/~lcls, 2000. Home/Search Document Not in Database Summary Related Articles Check |
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Overcoming instabilities in Verlet-I/r-RESPA with.. - Izaguirre, Ma.. Self-citation (Izaguirre Willcock Matthey Slabach Viamontes) (Correct)
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J. A. Izaguirre, J. Willcock, T. Matthey, T. B. Slabach, T. Steinbach, S. Stender, G. F. Viamontes, and J. Mohnke. ProtoMol: An object oriented framework for molecular dynamics. http://www.cse.nd.edu/~lcls, 2000.
Verlet-I/r-RESPA/Impulse Is Limited by Nonlinear Instability - Ma, Izaguirre, Skeel Self-citation (Izaguirre Ma) (Correct)
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J. A. Izaguirre, J. Willcock, T. Matthey, Q. Ma, T. B. Slabach, T. Steinbach, S. Stender, G. F. Viamontes, and J. Mohnke. ProtoMol: An object oriented framework for molecular dynamics. Available online via http://www.cse.nd.edu/lcls/Protomol.html, 2000.
Unknown - Protomol Molecular Dynamics Self-citation (Izaguirre Matthey) (Correct)
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J. A. Izaguirre, J. Willcock, T. Matthey, T. B. Slabach, T. Steinbach, S. Stender, G. F. Viamontes, and J. Mohnke. Protomol: An object oriented framework for molecular dynamics. http://www.cse.nd.edu/~lcls, 2000.
A Tutorial on the Prototyping of Multiple Time.. - Izaguirre.. (2001) Self-citation (Izaguirre Willcock Matthey Slabach Viamontes) (Correct)
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J. A. Izaguirre, J. Willcock, T. Matthey, T. B. Slabach, T. Steinbach, S. Stender, G. F. Viamontes, and J. Mohnke. ProtoMol: An object oriented framework for molecular dynamics. http://www.cse.nd.edu/~lcls, 2000.
ProtoMol: A Molecular Dynamics Framework with Incremental.. - Matthey, Izaguirre (2001) (2 citations) Self-citation (Izaguirre Matthey) (Correct)
....sizes are very large (thousands to hundreds of thousands of atoms) The time scale problem is typically addressed by using multiple time stepping integrators, whereas the second problem may be addressed through the use of parallel processing. In 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 ....
J. A. Izaguirre, J. Willcock, T. Matthey, T. B. Slabach, T. Steinbach, S. Stender, G. F. Viamontes, and J. Mohnke. Protomol: An object oriented framework for molecular dynamics. http://www.cse.nd.edu/~lcls, 2000.
Framework Design, Parallelization and Force Computation in.. - Matthey Self-citation (Matthey) (Correct)
....of MD obtained in the first part and the evaluation of advantages and drawbacks of existing MD programs. The main goal was to develop a flexible, extendable MD research platform, neither excluding run time efficiency nor parallelism. The design of the framework and its implementation PROTOMOL [63] were realized in collaboration with Jesus A. Izaguirre and his students. Furthermore, some design aspects were introduced from previous work with the object and component oriented graphics framework A set of classes that embodies an abstract design for solutions to a family of related ....
....i.e. up to 32. Details and results are presented in publication [D] 5 The PROTOMOL Framework MD programs may substantially differ in design or level of implementation, but they are essentially all based on Algorithm 1. The proposed MD component based framework distinguishes PROTOMOL [63] from other well known MD programs, such as GROMOS [119] Amber [121] CHARMM [15] A program with similar goals, which provided the initial idea behind PROTOMOL, is NAMD2 [66] However, NAMD2 s design goal is primarily high scalability. By revisiting and learning from these MD programs, three ....
[Article contains additional citation context not shown here]
J. A. Izaguirre, J. Willcock, T. Matthey, Q. Ma, T. B. Slabach, T. Steinbach, S. Stender, G. F. Viamontes, and J. Mohnke. PROTOMOL: An object oriented framework for molecular dynamics. Available online via http://www.cse.nd.edu/lcls/Protomol.html, 2000.
ProtoMol: A Molecular Dynamics Framework with Incremental.. - Matthey, Izaguirre (2000) (2 citations) Self-citation (Izaguirre Matthey) (Correct)
....sizes are very large (thousands to hundreds of thousands of atoms) The time scale problem is typically addressed by using multiple time stepping integrators, whereas the second problem may be addressed through the use of parallel processing. In 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 ....
J. A. Izaguirre, J. Willcock, T. Matthey, T. B. Slabach, T. Steinbach, S. Stender, G. F. Viamontes, and J. Mohnke. Protomol: An object oriented framework for molecular dynamics. http://www.cse.nd.edu/~lcls, 2000.
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