Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole...

Area of Science:

• Computational Chemistry
• Biophysics
• High-Performance Computing

Background:

• Molecular dynamics simulations are crucial for understanding biomolecular systems.
• Polarizable force fields, like AMOEBA, offer improved accuracy but are computationally expensive.
• Accelerating these simulations is essential for tackling larger and more complex biological problems.

Purpose of the Study:

• To extend the Tinker-HP package for Graphics Processing Unit (GPU) acceleration of molecular dynamics simulations.
• To implement and optimize the use of polarizable many-body force fields on GPU architectures.
• To evaluate the performance and scalability of the enhanced Tinker-HP package on various NVIDIA GPUs.

Main Methods:

• Development of a high-performance module using OpenACC and CUDA for GPU acceleration.
• Implementation of multiprecision arithmetic, comparing double precision with lower precision for performance and accuracy trade-offs.
• Benchmarking the Tinker-HP package on diverse NVIDIA GPU platforms (2080Ti, 3090, V100, A100) for single- and multi-GPU simulations.
• Testing on large biosystems containing millions of atoms.

Main Results:

• Demonstrated efficient single- and multiple-GPU utilization for molecular dynamics simulations.
• Showcased superior performance with lower precision arithmetic while maintaining accuracy for AMOEBA force field simulations.
• Achieved significant reductions in simulation time, establishing new performance benchmarks for AMOEBA.
• Validated scalability across various GPU architectures and system sizes.

Conclusions:

• The GPU-accelerated Tinker-HP package provides a powerful tool for efficient molecular dynamics simulations with polarizable force fields.
• The software enables faster and more accessible research in biophysics and related fields.
• Open-source release on GitHub facilitates community-driven development and application, including COVID-19 research efforts.