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18 documents found, showing 1 through 10. Next 10 →

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ProtoMol: A Molecular Dynamics Framework with Incremental Parallelization
by T. Matthey, J.A. Izaguirre — 2000 — In Proc. of the Tenth SIAM Conf. on Parallel Processing for Scientific Computing (PP01), Proceedings in Applied Mathematics
…\protomol_siam2001" 2000/12/4 page 1 i i i i i i i i ProtoMol: A Molecular Dynamics Framework…
Cited by 14 (8 self) – Add To MetaCart

ProtoMol: a molecular dynamics research framework for algorithmic development
by T. Matthey, A. Ko, J. A. Izaguirre — 2003 — in SpringerVerlag LNCS 2659, Computational Science-ICCS 2003
…PROTOMOL: A Molecular Dynamics Research Framework for Algorithmic Development T. Matthey , A. Ko…
Cited by 1 (1 self) – Add To MetaCart

A Tutorial on the Prototyping of Multiple Time Stepping Integrators for Molecular Dynamics
by Jesus A. Izaguirre, Thierry Matthey, Jeremiah Willcock, Qun Ma, Branden Moore, Thomas Slabach, George Viamontes — 2001
… performance. This is illustrated through the design of ProtoMol, an object-oriented component framework for MD…
Cited by 2 (2 self) – Add To MetaCart

Improved interpolation and system integration for FPGA-based molecular dynamics simulations
by Yongfeng Gu, Tom Vancourt, Martin C. Herbordt — 2006 — In Proc. Field Programmable Logic and Applications (2006
…-bonded force computation pipeline implemented on a 2004era COTS FPGA board and its integration into the ProtoMol…
Cited by 4 (3 self) – Add To MetaCart

Mdsimaid: An Automatic Recommender For Optimization Of Fast Electrostatic Algorithms For Molecular Simulations
by Alice N. Ko, Notre Dame, Jesús A. Izaguirre — 2002
… (Chemistry at HARvard Molecular Mechanics) and ProtoMol (a framework for molecular dynamics simulations…
Cited by 5 (2 self) – Add To MetaCart

Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse method
by Jesus A. Izaguirre, Qun Ma, Thierry Matthey, Jeremiah Willcock, Thomas Slabach, Branden Moore, George Viamontes
… may implement them into their MD codes, or use the program ProtoMol in which we have implemented…
Cited by 8 (5 self) – Add To MetaCart

MDSimAid: Automatic Parameter Optimization in Fast Electrostatic Algorithms
by Michael S. Crocker, Scott S. Hampton, Jesús A. Izaguirre — 2004 — J. Comp. Chem.In
…. MDSimAid is written in Python and uses ProtoMol [18] to test PME and MG. ProtoMol is a high- performance…
Cited by 1 (1 self) – Add To MetaCart

GIPSE: Streamlining the management of simulation on the grid
by J. M. Wozniak, A. Striegel, D. Salyers, J. A. Izaguirre — 2005 — In Proceedings of the 38th Annual Simulation Symposium. IEEE Computer Society
… Characteristic Networks Biology Application ns-2 [10] ProtoMol [11] Run Time Avg. 30 min. 7,200 min. Arguments 35…
Cited by 7 (3 self) – Add To MetaCart

PROTOMOL, an Object-Oriented Framework for Prototyping Novel Algorithms for Molecular Dynamics
by Thierry Matthey, Trevor Cickovski, Scott Hampton, Alice Ko, Qun Ma — 2002 — In Computational Science—ICCS 2003, International Conference
…, United States ProtoMol is a high-performance framework in C++ for rapid prototyping of novel algorithms…
Cited by 17 (12 self) – Add To MetaCart

Verlet-I/r-RESPA is limited by nonlinear instability
by Qun Ma, Jes Ús, A. Izaguirre, Robert, D. Skeel — 1951 — SIAM J. Sci. Comput
… ProtoMol [19, 30]. 1.4. Nonlinear instabilities in Verlet-I/r-RESPA/Impulse for unconstrained…
Cited by 3 (1 self) – Add To MetaCart

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