NAMD is the result of an interdisciplinary collaboration between Prof. Kale, computer science Prof. Robert D. Skeel, and physics Prof. Klaus J. Schulten at the Theoretical and Computational Biophysics Group (TCBG) of Beckman Institute.
NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code.
Charm++, developed by Prof. Kale and co-workers, simplifies parallel programming and provides automatic load balancing, which was crucial to the performance of NAMD.
In SC2002, Prof. Kale and co-authors James C. Phillips, Gengbin Zheng and Sameer Kumar, won a Gordon Bell Award for special accomplishment for their paper NAMD: Biomolecular Simulation on Thousands of Processors.
NAMD is implemented using the Converse runtime system, and the major components of NAMD are written in Charm++.
Converse provides machine-independent interface to all popular parallel computers as well as workstation clusters. Converse also implements a data-driven execution model, allowing parallel languages such as Charm++ to support the dynamic behavior of NAMD's chunk-based decomposition scheme.
The dynamic components of NAMD are implemented in the Charm++ parallel language. It is composed of collections of C++ objects, which communicate by remotely invoking methods on other objects. This supports the multi-partition decompositions in NAMD. Also data-driven execution adaptively overlaps communication and computation. Finally, NAMD benefits from Charm++'s load balancing framework to achieve unsurpassed parallel performance.
NAMD developers also extensively use the Projections, a performance visualization tool in Charm++, to diagnose and optimize the performance of NAMD.
The official NAMD home page is located at TCBG NAMD Research.
Outside of NAMD, we are experimenting with alternative ways to parallelize molecular dynamics computations.
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- 08-01
Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. Phillips, Gengbin Zheng, Laxmikant V. Kale, Overcoming Scaling Challenges in Biomolecular Simulations across Multiple Platforms, Proceedings of IEEE International Parallel and Distributed Processing Symposium 2008
- 07-10
Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. Phillips, Gengbin Zheng, Laxmikant V. Kale, NAMD: A Portable and Highly Scalable Program for Biomolecular Simulations, PPL Technical Report, 2007
- 07-05
Klaus Schulten, James C. Phillips, Laxmikant V. Kale, Abhinav Bhatele, Biomolecular modeling in the era of petascale computing, Petascale Computing: Algorithms and Applications, pp. 165-181, D. Bader, Ed., Chapman & Hall / CRC Press, New York, 2008
- 07-02
Sameer Kumar, Chao Huang, Gengbin Zheng, Eric Bohm, Abhinav Bhatele, James C. Phillips, Hao Yu, Laxmikant V. Kale, Scalable Molecular Dynamics with NAMD on Blue Gene/L, IBM Journal of Research and Development, Volume 52, No. 1/2, 2007
- 05-13
Sameer Kumar, Chao Huang, Gheorghe Almasi, Laxmikant V. Kale, Achieving Strong Scaling with NAMD on Blue Gene/L, Proceedings of IEEE International Parallel & Distributed Processing Symposium 2006
- 03-03
Laxmikant V. Kale, Sameer Kumar, Gengbin Zheng, Chee Wai Lee, Scaling Molecular Dynamics to 3000 Processors with Projections: A Performance Analysis Case Study, Terascale Performance Analysis Workshop, International Conference on Computational Science(ICCS), 2003
- 02-07
James C. Phillips, Gengbin Zheng, Sameer Kumar, Laxmikant V. Kale, NAMD: Biomolecular Simulation on Thousands of Processors, Proceedings of SC 2002
- 02-04
James Phillips, Gengbin Zheng, Laxmikant V. Kale, NAMD: Biomolecular Simulation on Thousands of Processors, Workshop: Scaling to New Heights
- 98-10
Tamar Schlick and Robert Skeel and Axel Brunger and Laxmikant Kale and John A. Board Jr. and Jan Jermans and Klaus Schulten , Algorithmic Challenges in Computational Molecular Biophysics , Journal of Computational Physics, Vol. 151, pp. 9-48, 1999.
- 98-05
James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind Bhandarkar, Neal Krawetz, Laxmikant Kale, Robert D. Skeel and Klaus Schulten, Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code, In book "Computational Molecular Dynamics: Challenges, Methods, Ideas"
- 98-04
Robert Brunner, Laxmikant Kale and James Phillips, Flexibility and Interoperability in a Parallel Molecular Dynamics Code, In book, "Object Oriented Methods for Inter-operable Scientific and Engineering Computing"
- 98-03
Laxmikant Kale, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten, NAMD2: Greater Scalability for Parallel Molecular Dynamics, Journal of Computational Physics
- 96-04
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kale, Robert D. Skeel, and Klaus Schulten , NAMD - a Parallel, Object-Oriented Molecular Dynamics Program, International Journal Supercomputing Applications and High Performance Computing, Winter 1996, Volume 10, number 4. Also, Beckman Institute Technical Report TB-95-17.
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