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High performance computing in biology: multimillion atom simulations of nanoscale systems
1Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, MS K710, Los Alamos, NM 87545, USA. kys@lanl.gov
Journal of Structural Biology
|December 26, 2006
Summary
Large-scale all-atom biomolecular simulations are now feasible. The NAMD program shows excellent performance for simulating millions of atoms, like the ribosome, on supercomputers.
Area of Science:
- Computational Biology
- Biophysics
- Molecular Dynamics
Background:
- All-atom simulations are computationally intensive, requiring significant compute load, communication speed, and memory.
- Advancements in electrostatic force calculation and dynamic load balancing have enabled simulations of large biomolecular complexes.
Purpose of the Study:
- To report simulation results for the ribosome, the largest all-atom biomolecular simulation to date.
- To measure the performance of the NAMD molecular dynamics simulation program on the Los Alamos National Laboratory Q Machine for various nano-scale systems.
Main Methods:
- All-atom molecular dynamics simulations were performed.
- The NAMD program was used to simulate systems up to approximately 2.64 million atoms.
- Performance was evaluated on the Los Alamos National Laboratory Q Machine using up to 1024 CPUs.
Main Results:
- The ribosome, with ~2.64 million atoms, represents the largest all-atom biomolecular simulation published.
- Multimillion atom systems are identified as a 'sweet spot' for the NAMD code on large supercomputers.
- NAMD achieved 85% parallel scaling efficiency for the ribosome system on 1024 CPUs.
Conclusions:
- Large-scale all-atom simulations of biomolecular complexes are achievable with current computational resources.
- The NAMD program demonstrates high performance and scalability for simulating massive biological systems.
- Targeted molecular dynamics simulations of the ribosome provide atomic-level insights into its conformational changes.
