Publications
How to Cite ProtoMol
T. Matthey, T. Cickovski, S. S. Hampton, A. Ko, Q. Ma, M. Nyerges,
T. Raeder, T. Slabach, and J. A. Izaguirre. ProtoMol: An
object-oriented framework for prototyping novel algorithms for
molecular dynamics. ACM Trans. Math. Softw., 30(3):237265, 2004.
Publications About ProtoMol
- Parallel Multigrid Summation for the N-body Problem, Jesús
A. Izaguirre and Scott S. Hampton and Thierry Matthey, in press,
Journal of Parallel and Distributed Computing, 2005.
- ProtoMol, an Object-Oriented Framework for Prototyping Novel
Algorithms for Molecular Dynamics, Thierry Matthey, Trevor
Cickovski, Scott Hampton, Alice Ko, Qun Ma, Matthew Nyerges, Troy
Raeder, Thomas Slabach and Jesús A. Izaguirre, ACM Transactions on
Mathematical Software, Vol. 20, No. 3, pp. 237-265, 2004.
- Design Patterns for Scientific Software, T. Cickovski,
T. Matthey, and J. A. Izaguirre, Technical Report TR-2004-29,
Department of Computer Science and Engineering, University of Notre
Dame, 2004.
- Framework Design, Parallelization and Force Computation in
Molecular Dynamics, Thierry Matthey. Ph.D. Thesis, Department of
Informatics, University of Bergen, Norway, Sept. 2002.
- ProtoMol: A Molecular Dynamics Framework with Incremental
Parallelization, Thierry Matthey and Jesús A. Izaguirre,
Proc. 10th SIAM Conference on Parallel Processing for Scientific
Computing, March 2001.
- A Tutorial on the Prototyping of Multiple Time Stepping
Integrators for Molecular Dynamics, Jesús A. Izaguirre,
Thierry Matthey, Jeremiah Willcock, Branden Moore, Qun Ma, Thomas
Slabach, and George Viamontes, 2001.
Publications Citing ProtoMol
- MDSimAid: Automatic Parameter Optimization in Fast Electrostatic
Algorithms, Michael S. Crocker, Scott S. Hampton, Thierry
Matthey, and Jesús A. Izaguirre, Journal of Computational Chemistry,
Vol. 26, pp. 1021-1031, 2005.
- Shadow Hybrid Monte Carlo: An Efficient Propagator in Phase Space
of Macromolecules, Jesús A. Izaguirre and Scott S. Hampton,
Journal of Computational Physics, Vol. 200, No. 2, pp. 581-604, 2004.
- Improved Sampling for Biological Molecules Using Shadow Hybrid
Monte Carlo, Scott S. Hampton and Jesús A. Izaguirre, In
M. Bubak, G. D. von Albada, and P. M. A. Sloot; J. J. Dongarra,
editors, 4th International Conference on Computational Science,
Kraków, Poland, volume 3037 of Lecture Notes in Computer Science,
pp. 268-274. Springer-Verlag, New York, 2004.
- Polarizable Force Fields for Flexible Molecules, Asbjřrn
Holt, M.S. Thesis, NTNU and Lunds Univesitet, Norway, July 2004.
- Multikomponent Coulumbkrystaller: Eksperimenter og Simulationer,
Esben S. Nielsen, Cand. Scient., University Aarhus, August 2004
- Improved Sampling of Configuration Space of Biomolecules using
Shadow Hybrid Monte Carlo, Scott S. Hampton, M.S. Thesis,
Department of Computer Science and Engineering, University of Notre
Dame, August 2004.
- Coulomb bicrystals of species with identical charge-to-mass
ratios, T. Matthey, J.P. Hansen, M. Drewsen, Phys. Rev Lett, 91 No. 16
165001, 2003.
- Verlet-I/r-RESPA is limited by nonlinear instability, Qun
Ma, Jesús A. Izaguirre and Robert D. Skeel, SIAM Journal on Scientific
Computing, Vol. 24, No. 6, pp. 1951-1973, May 6, 2003.
- Long time step molecular dynamics using targeted Langevin
stabilization, Qun Ma and Jesús A. Izaguirre, Proceedings of the
ACM Symposium on Applied Computing SAC 03, pp. 178-182, 2003.
- Nonlinear instability in multiple time stepping molecular
dynamics, Qun Ma, Jesús A. Izaguirre and Robert D. Skeel,
Proceedings of the ACM Symposium on Applied Computing SAC 03,
pp. 167-171, 2003.
- MDSimAid : Automatic Optimization of Fast Electrostatics
Algorithms for Molecular Simulations, Alice N. Ko and Jesús
A. Izaguirre, International Conference on Computational Science ICCS
2003.
- Novel Multiscale Algorithms for Molecular Dynamics, Qun Ma,
Ph.D. Thesis, Department of Computer Science and Engineering,
University of Notre Dame, June, 2003.
- Eksperiment og simulering av ugelstadkuler i en magnetisk vćske,
A. Hellesřy, M.S. Thesis, Department of Physics, University of Bergen, 2002.
- Overcoming instabilities in Verlet-I/r-RESPA with the mollified
impulse method (PS), Jesús A. Izaguirre, Qun Ma, Thierry Matthey,
Jeremiah Willcock, Thomas Slabach, Branden Moore, and George
Viamontes, Computational Methods for Macromolecules: Challenges and
Applications, Proceedings of the 3rd International Workshop on
Algorithms for Macromolecular Modeling, New York, Oct. 12-14,
2000. Lecture Notes in Computational Science and Engineering (LNCSE),
Vol. 24, pp. 146-174. Springer Verlag, Berlin, 2002. Editors:
T. Schlick and H. H. Gan
- MDSimAid: An Automatic Recommender for Optimization of Fast
Electrostatic Algorithms for Molecular Simulations, Alice
N. Ko. M.S. Thesis, Department of Computer Science and Engineering,
Notre Dame, IN, Dec. 2002.