Table 1. Details of all simulations run for the trimer, dodecamer and 20-mer systems.
| Length of OPEP simulations (ns)(a) | OPEP - LABEL of structures extracted(b) | Temperatures min-max (K) & number of temperatures(c) | GROMACS - LABEL of reconstructed OPEP extracted structures(b) | Length of GROMACS simulations (ns)(d) | Total number of atoms(e) | Temperature (K)(f) | |
| 3-mer | 50×16 | 03OP1-A | 222.5–525 16 | 03-GR1-A | 100 | 6504 | 300 |
| 03OP1-B | 222.5–525 16 | 03-GR1-B | 100 | 5997 | 300 | ||
| 03OP1-C | 222.5–525 16 | 03-GR1-C | 100 | 5619 | 300 | ||
| 03OP1-D | 222.5–525 16 | 03-GR1-D | 100 | 5949 | 300 | ||
| 03OP1-E | 222.5–525 16 | 03-GR1-E | 100 | 6621 | 300 | ||
| 12-mer | 125×16 | 12OP1-A | 222.5–525 16 | 12-GR1-A | 100 | 56271 | 300 |
| 12OP1-B | 222.5–525 16 | 12-GR1-B | 100 | 40476 | 300 | ||
| 12OP1-C | 222.5–525 16 | 12-GR1-C | 100 | 15381 | 300 | ||
| 12OP1-D | 222.5–525 16 | 12-GR1-D | 100 | 16134 | 300 | ||
| 12OP1-E | 222.5–525 16 | 12-GR1-E | 100 | 17157 | 300 | ||
| 20-mer OPp | 200×20 | 20OPp-A | 234.6–447.6 20 | 20GRp-A1 | 100 | 25620 | 300 |
| 20OPp-A | 234.6–447.6 20 | 20GRp-A2 | 100 | 25620 | 300 | ||
| 20OPp-B | 234.6–447.6 20 | 20GRp-B1 | 100 | 27816 | 300 | ||
| 20OPp-B | 234.6–447.6 20 | 20GRp-B2 | 100 | 27816 | 300 | ||
| 20OPp-B | 234.6–447.6 20 | 20GRp-B3 (REMD) | 10×12 | 27816 | see text | ||
| 20OPp-C | 234.6–447.6 20 | 20GRp-C1 | 100 | 49674 | 300 | ||
| 20OPp-C | 234.6–447.6 20 | 20GRp-C2 | 100 | 49674 | 300 | ||
| 20OPp-D | 234.6–447.6 20 | 20GRp-D1 | 100 | 23746 | 300 | ||
| 20OPp-D | 234.6–447.6 20 | 20GRp-D2 | 100 | 23746 | 300 | ||
| 20-mer OP2 | 400×22 | 20OP2-A | 223.8–425.9 22 | 20GR2-A | 100 | 21586 | 300 |
| 20OP2-B | 223.8–425.9 22 | 20GR2-B | 100 | 24640 | 300 | ||
| 20OP2-C | 223.8–425.9 22 | 20GR2-C | 100 | 23554 | 300 | ||
| 20OP2-E | 223.8–425.9 22 | 20GR2-E | 100 | 26065 | 300 | ||
| 20OP2-N | 223.8–425.9 22 | 20GR2-N1 | 100 | 32206 | 300 | ||
| 20OP2-N | 223.8–425.9 22 | 20GR2-N2 (REMD) | 10×12 | 32206 | see text |
This table presents simulations done with OPEP (coarse-grained potential) and GROMACS (all-atom potential).
The total simulation time for OPEP REMD simulations in the format time_per_replica x number_of_replicas.
The label of the OPEP/GROMACS structures extracted. The label indicates the number of monomers, the potential used (OP for OPEP and GR for GROMACS), the simulation index (1,2 or p (preliminary)) and the letter ID of the structure.
The range of temperatures (in K) used for OPEP REMD simulations.
The total simulation time for GROMACS simulations. MD simulations are indicated by only one number while, for REMD simulations, the total simulation time is given in the format time_per_replica x number_of_replicas.
The total number of atoms in the system including protein and solvatation water atoms.
The temperature used in GROMACS simulations (in K).