MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with...

Area of Science:

• Computational Chemistry
• Biophysics
• Materials Science

Background:

• Molecular dynamics (MD) simulations are crucial for understanding molecular behavior.
• Simulating very large systems (millions of atoms) presents significant computational challenges.

Purpose of the Study:

• Introduce MODYLAS, a new general-purpose MD simulation program.
• Address the need for efficient simulation of large-scale physical, chemical, and biological systems.

Main Methods:

• Employs rigorous long-range force evaluation using the fast multipole method (FMM).
• Incorporates novel methods for fine-grained parallelism, including buffering-free communications and minimal latency algorithms.
• Utilizes blockwise arithmetic operations to minimize cache misses.

Main Results:

• MODYLAS demonstrates excellent scalability on the K-computer with 65,536 nodes.
• Achieves a calculation time of approximately 5 ms per MD step for a 10 million-atom system.
• Enables computation of 35 ns of simulation time per day.

Conclusions:

• MODYLAS is a highly scalable and efficient MD program for large systems.
• Facilitates the investigation of complex systems like viruses, proteins, and polymers.
• Advances the capabilities of computational science in physical, chemical, and biological research.