Table 1.
Benchmark Results.
| Molecule | Atoms | Force field | Platform | Ns/day | Improvement |
|---|---|---|---|---|---|
| fip35 | 544 | parm03 | CPU/AMBER | 4.5 | – |
| fip35 | 544 | parm03 | ATI | 279.2 | 62 |
| fip35 | 544 | parm03 | Nvidia | 576.2 | 128 |
| Villin | 582 | parm03 | CPU/AMBER | 3.9 | – |
| Villin | 582 | parm03 | ATI | 260.8 | 67 |
| Villin | 582 | parm03 | Nvidia | 528.5 | 136 |
| Lambda | 1254 | parm03 | CPU/AMBER | 0.79 | – |
| Lambda | 1254 | parm03 | ATI | 141.7 | 179 |
| Lambda | 1254 | parm03 | Nvidia | 201.6 | 255 |
| α-spectrin | 5078 | parm99 | CPU/AMBER | 0.023 | – |
| α-spectrin | 5078 | parm99 | ATI | 14.2 | 617 |
| α-spectrin | 5078 | parm99 | Nvidia | 16.9 | 735 |
Improvement is the speedup obtained by running on the GPU versus running AMBER on the CPU.
ATI: Radeon HD 4870 GPU.
Nvidia: GeForce GTX 280 GPU.