Tinker-HP

Tinker-HP accelerates molecular dynamics simulations of large biomolecular systems by providing GPU- and CPU-accelerated, massively parallel implementations of polarizable many-body force fields (AMOEBA) for high-performance computation.

Key Features:

• GPU Acceleration: Implements single- and multi-GPU execution to accelerate simulations on GPU hardware and complements CPU execution for hybrid workflows.
• Scalable Strategy: Uses OpenACC and CUDA to achieve scalable performance across diverse GPU platforms, including NVIDIA 2080Ti, 3090, V100, and A100 cards.
• Multiprecision Capabilities: Supports multiprecision arithmetic with double precision for reference computations and lower-precision modes to improve performance while preserving comparable accuracy.
• AMOEBA Force Field Implementation: Implements the AMOEBA point dipole polarizable many-body force field for accurate modeling of molecular interactions.
• Performance Benchmarks: Provides benchmarking results on NVIDIA GPU platforms demonstrating substantial reductions in computation time relative to prior AMOEBA implementations.
• Strong Scaling and Parallelization: Supports strong-scaling across multiple nodes to enable massive parallelization for large-scale simulations.
• Adaptive Sampling and Large-Scale Applicability: Integrates unsupervised adaptive sampling techniques to extend applicability to large and complex biophysical systems.

Scientific Applications:

• Molecular dynamics of large systems: Enables atomistic MD simulations of large biomolecular assemblies using polarizable force fields.
• Modeling biomolecular interactions: Facilitates accurate modeling of molecular interactions and many-body polarization effects at the atomic level with AMOEBA.
• High-throughput biophysical studies: Accelerates computational analyses for large-scale research efforts, including investigations related to COVID-19.

Methodology:

Uses OpenACC and CUDA for GPU parallelization; supports single- and multi-GPU execution and multi-node strong-scaling; implements multiprecision arithmetic (double and lower-precision modes); executes the AMOEBA point dipole polarizable force field and incorporates unsupervised adaptive sampling.