Table 1.
Summary for the setup details of the six 200-ns MD runs at 315 K for three different systems S, P, and F. For each system, we describe the name of the system, the initial membrane insertion state of pHLIP, the name of MD runs, the initial state of each MD run, the total number of atoms, the size of simulation box and the length of each MD run.
| System | Insertion state of pHLIP | Name of MD run | Initial state | Number of atoms | Simulation box size (nm3) | Length of MD run (ns) |
|---|---|---|---|---|---|---|
| S | Surface | S (acidic) | Figure 1a | 27,083 | 6.6 × 6.5 × 9.0 | 200 |
| Surface | S (basic) | Figure 1b | 27,066 | 6.6 × 6.5 × 9.0 | 200 | |
|
| ||||||
| P | Partial insertion | P (acidic) | Figure 2a | 24,347 | 6.5 × 6.5 × 9.0 | 200 |
| Partial insertion | P (basic) | Figure 2b | 24,345 | 6.5 × 6.5 × 9.0 | 200 | |
|
| ||||||
| F | Full insertion | F (acidic) | Figure 4a | 16,808 | 6.4 × 6.3 × 6.5 | 200 |
| Full insertion | F (basic) | Figure 4b | 16,789 | 6.4 × 6.3 × 6.5 | 200 | |