Recent breakthroughs in GPU Acceleration for High-Performance Computing (HPC) have yielded rapid advancements in the domain of Molecular Dynamics (MD). Such MD simulations commonly constitute 100,000 atoms, while numerous published NAMD simulations have exceeded 10,000,000 atoms. Proper research of even the most basic bio-molecular machines typically depend on simulations of 100 ns or longer. Typically the most time-consuming calculations in molecular dynamics are the force calculations between non-bonded atoms. To aid this, GPUs are the perfect solution due to the inherent high degree of parallelism and floating-point arithmetic capability. Typically GPU Accelerated NAMD Simulations attain performance levels up to twenty times that of a single CPU core, thereby decreasing the runtime for the non-bonded force calculations, such that it can complement bonded forces and PME long-range force calculations on that utilize the CPU.
System Specs: 2 x Intel Xeon Gold 6148 2.4GHz CPU, 192GB DDR4-2666, 3x480GB SSD w/RAID 0, NVIDIA Titan V 12GB GPU