Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

TLDR

The authors implement a generalized Born implicit‑solvent molecular dynamics engine in AMBER that runs entirely on CUDA‑enabled NVIDIA GPUs, aiming to evaluate both performance gains and the impact of different precision models on simulation outcomes. The implementation employs GPU‑optimized algorithms, supports single‑precision, mixed‑precision, and double‑precision force calculations, and is benchmarked against conventional CPU clusters to demonstrate speedups. Tests show that the mixed‑precision SPDP model yields results comparable to full double precision while avoiding the large numerical noise of pure single precision, and that the GPU implementation achieves performance on a single desktop that rivals or exceeds traditional supercomputers.

Abstract

We present an implementation of generalized Born implicit solvent all-atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA enabled NVIDIA graphics processing units (GPUs). We discuss the algorithms that are used to exploit the processing power of the GPUs and show the performance that can be achieved in comparison to simulations on conventional CPU clusters. The implementation supports three different precision models in which the contributions to the forces are calculated in single precision floating point arithmetic but accumulated in double precision (SPDP), or everything is computed in single precision (SPSP) or double precision (DPDP). In addition to performance, we have focused on understanding the implications of the different precision models on the outcome of implicit solvent MD simulations. We show results for a range of tests including the accuracy of single point force evaluations and energy conservation as well as structural properties pertainining to protein dynamics. The numerical noise due to rounding errors within the SPSP precision model is sufficiently large to lead to an accumulation of errors which can result in unphysical trajectories for long time scale simulations. We recommend the use of the mixed-precision SPDP model since the numerical results obtained are comparable with those of the full double precision DPDP model and the reference double precision CPU implementation but at significantly reduced computational cost. Our implementation provides performance for GB simulations on a single desktop that is on par with, and in some cases exceeds, that of traditional supercomputers.