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. 2020 Dec 7;5(50):32823–32843. doi: 10.1021/acsomega.0c05469

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
a

All data points were obtained in 200 ns simulations. (+) Minimal bond rescaling. (++) Important bond rescaling. (+++) All bonds rescaled.

b

Using standard desktop machines, see Supporting Information and Table S2 for simulations parameters and hardware specifications.