Scientific Applications: NAMD - Molecular Dynamics
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.

People
Papers/Talks
13-43
2013
[Paper]
Parallel Science and Engineering Applications: The Charm++ Approach: Chapter 4: Scalable Molecular Dynamics with NAMD [Book 2013]
| James Phillips | Klaus Schulten | Abhinav Bhatele | Chao Mei | Yanhua Sun | Eric Bohm | Laxmikant Kale
13-16
2013
[Paper]
Parallel Science and Engineering Applications: The Charm++ Approach [Book 2013]
12-33
2012
[Paper]
Optimizing Fine-grained Communication in a Biomolecular Simulation Application on Cray XK6 [SC 2012]
| Yanhua Sun | Gengbin Zheng | Chao Mei | Eric Bohm | James Phillips | Terry Jones | Laxmikant Kale
11-50
2012
[Paper]
A uGNI-Based Asynchronous Message-driven Runtime System for Cray Supercomputers with Gemini Interconnect [IPDPS 2012]
| Yanhua Sun | Gengbin Zheng | Ryan Olson | Terry Jones | Laxmikant Kale
11-17
2011
[Paper]
Enabling and Scaling Biomolecular Simulations of 100~Million Atoms on Petascale Machines with a Multicore-optimized Message-driven Runtime [SC 2011]
| Chao Mei | Yanhua Sun | Gengbin Zheng | Eric Bohm | Laxmikant Kale | James Phillips | Chris Harrison
11-14
2011
[Poster]
Molecular dynamics simulations on supercomputers performing 10^18 flop/s [UIUC Postdoc Symposium 2011]
| Abhinav Bhatele | William Gropp | Laxmikant Kale
10-25
2011
[Paper]
NAnoscale Molecular Dynamics (NAMD) [Encyclopedia of Parallel Computing 2011]
| Laxmikant Kale | Abhinav Bhatele | Eric Bohm | James Phillips
10-20
2010
[Paper]
Periodic Hierarchical Load Balancing for Large Supercomputers [IJHPCA 2010]
10-15
2010
[Paper]
Simulating Large Scale Parallel Applications using Statistical Models for Sequential Execution Blocks [ICPADS 2010]
10-08
2010
[Paper]
Hierarchical Load Balancing for Charm++ Applications on Large Supercomputers [P2S2 2010]
09-15
2009
[Poster]
Performance Comparison of Intrepid, Jaguar and Ranger using Scientific Applications [SC 2009]
09-02
2009
[Paper]
Dynamic Topology Aware Load Balancing Algorithms for Molecular Dynamics Applications [ICS 2009]
08-01
2008
[Paper]
Overcoming Scaling Challenges in Biomolecular Simulations across Multiple Platforms [IPDPS 2008]
07-10
2007
[Paper]
NAMD: A Portable and Highly Scalable Program for Biomolecular Simulations [Computer Science Research and Technical Reports 2007]
07-05
2008
[Paper]
Biomolecular modeling in the era of petascale computing [Petascale Computing: Algorithms and Applications 2008]
| Klaus Schulten | James Phillips | Laxmikant Kale | Abhinav Bhatele
07-02
2007
[Paper]
Scalable Molecular Dynamics with NAMD on Blue Gene/L [IBM Journal of Research and Development 2007]
06-20
2006
[Poster]
Charm++ on Cell [PPL Poster 2006]
06-19
2006
[Poster]
Charm++ Simplifies Programming for the Cell Processor [SC 2006]
05-26
2005
[Poster]
Speeding Up Parallel Simulation with Automatic Load Balancing [PPL Poster 2005]
| Hari Govind | Gengbin Zheng | Laxmikant Kale | Michael Breitenfeld | Philippe Geubelle
05-13
2006
[Paper]
Achieving Strong Scaling with NAMD on Blue Gene/L [IPDPS 2006]
| Sameer Kumar | Chao Huang | Gheorghe Almasi | Laxmikant Kale
04-11
2004
[MS Thesis]
LeanMD: A Charm++ framework for high performance molecular dynamics simulation on large parallel machines [Thesis 2004]
03-03
2003
[Paper]
Scaling Molecular Dynamics to 3000 Processors with Projections: A Performance Analysis Case Study [Workshop on Terascale Performance Analysis at ICCS 2003]
02-07
2002
[Paper]
NAMD: Biomolecular Simulation on Thousands of Processors [SC 2002]
| James Phillips | Gengbin Zheng | Sameer Kumar | Laxmikant Kale
02-04
2002
[Paper]
NAMD: Biomolecular Simulation on Thousands of Processors [Scaling to New Heights Workshop at Pittsburgh Supercomputing Center 2002]
| James Phillips | Gengbin Zheng | Laxmikant Kale
98-10
1999
[Paper]
Algorithmic Challenges in Computational Molecular Biophysics [Journal of Computational Physics 1999]
| Tamar Schlick | Robert Skeel | Axel Brunger | Laxmikant Kale | John Board Jr. | Jan Hermans | Klaus Schulten
98-08
1998
[Paper]
NAMD: A Case Study in Multilingual Parallel Programming [LCPC 1998]
| Laxmikant Kale | Milind Bhandarkar | Robert Brunner | Neal Krawetz | J. Philips | Aritomo Shinozaki
98-06
1998
[Paper]
Computational biophysics today [Journal of Computational Physics 1998]
| Tamar Schlick | Robert Skeel | Axel Brunger | Klaus Schulten | Laxmikant Kale | Jan Hermans | John Board Jr.
98-05
1998
[Paper]
Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code [LNCS 1998]
| James Phillips | Robert Brunner | Aritomo Shinozaki | Milind Bhandarkar | Neal Krawetz | Laxmikant Kale | Robert Skeel | Klaus Schulten
98-04
1998
[Paper]
Flexibility and Interoperability in a Parallel Molecular Dynamics Code [Object Oriented Methods for Inter-operable Scientific and Engineering Computing 1998]
| Robert Brunner | Laxmikant Kale | James Phillips
98-03
1998
[Paper]
NAMD2: Greater Scalability for Parallel Molecular Dynamics [Journal of Computational Physics 1998]
| Laxmikant Kale | Robert Skeel | Milind Bhandarkar | Robert Brunner | Attila Gursoy | Neal Krawetz | James Phillips | Aritomo Shinozaki | Krishnan Varadarajan | Klaus Schulten
98-02
1998
[Paper]
Load Balancing in Parallel Molecular Dynamics [International Symposium on Solving Irregularly Structured Problems in Parallel 1998]
96-04
1996
[Paper]
NAMD - a Parallel, Object-Oriented Molecular Dynamics Program [International Journal Supercomputing Applications and High Performance Computing 1996]
| M. Nelson | William Humphrey | Attila Gursoy | A. Dalke | Laxmikant Kale | Robert Skeel | Klaus Schulten
94-02
1994
[Paper]
Modeling Biomolecules: Larger Scales, Longer Durations [IEEECSE 1994]
| John Board Jr. | Laxmikant Kale | Klaus Schulten | Robert Skeel | Tamar Schlick