Development of hardware accelerator for molecular dynamics simulations: A computation board that calculates nonbonded interactions in cooperation with fast multipole method

Abstract

Evaluation of long-range Coulombic interactions still represents a bottleneck in the molecular dynamics (MD) simulations of biological macromolecules. Despite the advent of sophisticated fast algorithms, such as the fast multipole method (FMM), accurate simulations still demand a great amount of computation time due to the accuracy/speed trade-off inherently involved in these algorithms. Unless higher order multipole expansions, which are extremely expensive to evaluate, are employed, a large amount of the execution time is still spent in directly calculating particle-particle interactions within the nearby region of each particle. To reduce this execution time for pair interactions, we developed a computation unit (board), called MD-Engine II, that calculates nonbonded pairwise interactions using a specially designed hardware. Four custom arithmetic-processors and a processor for memory manipulation ("particle processor") are mounted on the computation board. The arithmetic processors are responsible for calculation of the pair interactions. The particle processor plays a central role in realizing efficient cooperation with the FMM. The results of a series of 50-ps MD simulations of a protein-water system (50,764 atoms) indicated that a more stringent setting of accuracy in FMM computation, compared with those previously reported, was required for accurate simulations over long time periods. Such a level of accuracy was efficiently achieved using the cooperative calculations of the FMM and MD-Engine II. On an Alpha 21264 PC, the FMM computation at a moderate but tolerable level of accuracy was accelerated by a factor of 16.0 using three boards. At a high level of accuracy, the cooperative calculation achieved a 22.7-fold acceleration over the corresponding conventional FMM calculation. In the cooperative calculations of the FMM and MD-Engine II, it was possible to achieve more accurate computation at a comparable execution time by incorporating larger nearby regions.

Ursolic acid, an antagonist for transforming growth factor (TGF)-$beta;1

“…Temperature was controlled at 300 K during simulations and no coulomb cut-off was applied. To accelerate calculations, a special-purpose parallel computer for nonbonded force sum, MD-Engine was used [24]. Total computing times were about 11 days.…”

Solvent Site-Dipole Field Accompanying Protein-Ligand Approach Process

“…All of the electrostatic interactions in the system were exactly computed at every step of simulation without truncation. We used a special purpose computer, MD Engine II [23][24], developed to accelerate the computation of non-bonded interactions.…”

An Automated Framework for Accelerating Numerical Algorithms on Reconfigurable Platforms Using Algorithmic/Architectural Optimization

“…A naive calculation of the interactions at all target particles takes O(N 2 ) arithmetic operations. Existing accelerators include GRAPE (GRAvity PipE) project [18], MD-GRAPE [19], [20], MD Engine [21], [22]. All these hardware systems are specialized ASIC based solutions for specific N-body applications.…”