Table 2. Average Rg Obtained for CG Models of the Benchmark Optimized Using Execution Mode 1 and Swarm-CG Default Settings, the Reference AA-Mapped Trajectories and Manually Parameterized CG Models from the Literaturea.
| radius of gyration (Rg) |
|||||
|---|---|---|---|---|---|
| molecule | bond scaling | ref. AA model [Å] | optimized CG model error [ΔÅ] (Δ%) | manually parametrized CG model error [ΔÅ] (Δ%) | optimization wall timeb (h) |
| BTA | ++ | 9.07 | 0.37 (4.1%) | 0.41 (4.5%)83 | 6 |
| BTT | ++ | 8.45 | 0.73 (8.6%) | 0.89 (10.5%)84 | 7 |
| NDI | +++ | 10.98 | 0.53 (4.8%) | 0.75 (6.8%)47 | 16.5 |
| porphyrin | ++ | 13.58 | 0.40 (3.0%) | 0.60 (4.4%)50 | 15.5 |
| β-cyclodextrin | n/a | 5.71 | 0.15 (2.6%) | 0.35 (6.1%)97 | 5 |
| pillar[5]arene | + | 6.43 | 0.07 (1.1%) | n/a | 6.5 |
| spermine dendron | + | 9.50 | 0.27 (2.8%) | n/a | 12 |
| PAMAM G1 | n/a | 9.95 | 0.12 (1.2%) | 2.62 (26.3%)49 | 5 |
| PAMAM G2 | n/a | 13.61 | 1.26 (9.3%) | 3.32 (24.4%)49 | 5.5 |
All data points were obtained in 200 ns simulations. (+) Minimal bond rescaling. (++) Important bond rescaling. (+++) All bonds rescaled.
Using standard desktop machines, see Supporting Information and Table S2 for simulations parameters and hardware specifications.