Table 1.
Protocols for IT-TI calculations
| Reference Name | Elec / vdW No. λ |
Initialization | Non-Bonded | Decoupling | Runs × Time/λ (ns) |
Total Time (ns) |
|---|---|---|---|---|---|---|
| medium cont/simul/14λ a | 9 / 14 | continuous | simultaneous | inter + intra | 20 × 1 | 280 |
| long cont/simul/14λ | 9 / 14 | continuous | simultaneous | inter + intra | 10 × 2 | 280 |
| medium cont/simul/inter/14λ | 9 / 14 | continuous | simultaneous | inter only | 20 × 1 | 280 |
| medium cont/sep/14λ | 9 / 5 | continuous | separate | inter + intra | 20 × 1 | 280 |
| medium cont/sep/19λ b | 9 / 10 | continuous | separate | inter + intra | 20 × 1 | 380 |
| medium parall/simul/14λ | 9 / 14 | parallel* | simultaneous | inter + intra | 20 × 1 | 280 |
| medium parall/simul/19λ | 9 / 19 | parallel* | simultaneous | inter + intra | 20 × 1 | 380 |
| medium parall/simul/inter/14λ | 9 / 14 | parallel* | simultaneous | inter only | 20 × 1 | 280 |
| medium parall/sep/14λ | 9 / 5 | parallel* | separate | inter + intra | 20 × 1 | 280 |
| medium parall/sep/19λ | 9 / 10 | parallel* | separate | inter + intra | 20 × 1 | 380 |
| long parall/sep/19λ | 9 / 10 | parallel* | separate | inter + intra | 10 × 2 | 380 |
a
For N1, 14 λ =[0, 0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0,4, 0.5, 0.6, 0.7, 0.8, 0.9, 1]; for RmlC [0, 0.1, 0.2, 0.25, 0.3, 0.37, 0.45, 0.5, 0.65, 0.75, 0.8, 0.9, 0.97, 1].
b
For N1, 19 λ adds [0.55, 0.65, 0.75, 0.85, 0.95]; for RmlC [0.05, 0.15, 0.6, 0.7, 0.85].
*
Protocols are well-suited for distributed computing.