Table 1. Computational Cost and Wall Clock Time for Simulations of Ligand-Protein Complex Using Equilibrium and Nonequilibrium Methods.
| method | protocol | total simulation | wall clock timea | |
|---|---|---|---|---|
| equilibrium | 5 replicas | 260 ns | ∼45 min | |
| 13 λ-windows | ||||
| 4 ns production run for each window | ||||
| nonequilibrium | equilibrium runs: | nonequilibrium transition: | 500 ns (150 ns)b | ∼135 min(∼115 min)b |
| 2 end points | 2 directions | |||
| 5 replicas | 100 runs each direction | |||
| 10 ns per replica | 2 ns (250 ps)b each run | |||
a
All individual runs are executed concurrently wherever possible. Wall clock time is shown as the execution time on ALCF’s Polaris, an HPE Apollo 6500 Gen10+ system equipped with NVIDIA A100 GPU accelerators.
b
Simulation protocol recommended from current study (see Results section).