Table 3. Data Used for the Benchmarking of Swarm-CG Using Default Settings.
| reference AA trajectory |
||||||
|---|---|---|---|---|---|---|
| molecule | simulation time (μs) | number of frames | force field | solvent | nonbonded parametrizationa | used for manual parametrization evaluation |
| BTA | 1 | 5000 | GAFF126+ TIP3P127 | Water | MARTINI 2.283 | yes |
| BTT | 1 | 5000 | GAFF126+ TIP3P127 | Water | MARTINI 2.284 | yes |
| NDI | 1 | 5000 | GAFF126 | cyclohexane | MARTINI 2.247 | yes |
| porphyrin | 1 | 5000 | GAFF126 | cyclohexane | MARTINI 2.250 | yes |
| β-cyclodextrin | 1 | 5000 | q4md-CD128+ TIP3P127 | Water | MARTINI 2.197 | yes |
| pillar[5]arene | 1 | 5000 | GAFF126+ TIP3P127 | Water | MARTINI 2.2129 | no |
| spermine dendron | 1 | 5000 | GAFF126+ TIP3P127 | Water | MARTINI 2.2129 | no |
| PAMAM G1 | 1 | 5000 | GAFF126+ TIP3P127 | Water | MARTINI 2.249 | yes |
| PAMAM G2 | 1 | 5000 | GAFF126+ TIP3P127 | Water | MARTINI 2.249 | yes |
a
Where present, nonbonded interactions were further tuned as described in the associated literature, starting from the cited force field.