Table 9. Performance of the refinement benchmarks for = 0.2 nm on two hardware configurations.
| System | D (×106) | N (×106) | W (ns/d) | S (ns/d) | TS (days, short) | TS (days, long) |
|---|---|---|---|---|---|---|
| Aldolase | 1.3 | 0.11 | 33.4 | 39.9 | 1.0 | 1.8 |
| Tubulin | 0.2 | 0.09 | 87.0 | 110.9 | 0.4 | 0.6 |
| TRPV1 | 1.9 | 0.37 | 16.7 | 21.5 | 2.0 | 3.3 |
| Nucleosome* | 0.6 | 0.17 | 20.7 | 29.9 | 1.3 | 2.3 |
| NSF | 1.3 | 0.36 | 18.5 | 24.9 | 1.6 | 2.8 |
| CorA | 1.2 | 0.31 | 25.4 | 29.7 | 1.3 | 2.4 |
| 70S Ribosome | 64.0 | 3.10 | 1.4 | 2.1 | 19.1 | n/a |
D = number of cryo-EM density grid points, N = number of atoms including water and ions, W = 6 core workstation with one Intel E5-1650v4 @ 3.6 GHz CPU and one NVIDIA GTX 980 GPU, = 24 core server node with two Intel Gold 6146 @ 3.2 GHz CPUs and two GTX 1080Ti GPUs. TS = total run time for the short (40 ns) and long (70 ns) protocols in days using the S hardware configuration (see Figure 2—figure supplement 1). The run times do not include setting up the simulated systems or batch queuing times.
*2-fs time step was used.