Table 2:
List of ΔVavg, σΔV and k0P values obtained by GaMD simulations of alanine dipeptide. (A) The results were collected from conventional GaMD simulations with a fixed threshold energy and σ0P value. (B) The results were collected from force constant rex-GaMD simulations with the exchange of σ0P within 1.0 to 1.6 kcal/mol. Three independent simulations were performed. The ΔVavg and σΔV values were calculated at the stage of σ0P=1.0 kcal/mol. (C) The results were collected from threshold energy rex-GaMD simulations. The threshold energy was switched between lower and upper bound. The ΔVavg and σΔV values were collected when threshold energy was at the lower bound.
| (A) | ||||
|---|---|---|---|---|
| σ0P (kcal/mol) | threshold E | ΔVavg (kcal/mol) | σΔV (kcal/mol) | k0P |
| 1.0 | lower bound | 2.197 | 1.130 | 0.178 |
| 1.1 | lower bound | 2.422 | 1.129 | 0.264 |
| 1.2 | lower bound | 2.563 | 1.397 | 0.362 |
| 1.3 | lower bound | 3.126 | 1.583 | 0.434 |
| 1.4 | lower bound | 3.332 | 1.679 | 0.542 |
| 1.5 | lower bound | 3.410 | 1.771 | 0.789 |
| 1.6 | lower bound | 3.672 | 1.841 | 1.000 |
| 1.0 | upper bound | 2.570 | 1.132 | 0.130 |
| (B) | ||||
| σ0P (kcal/mol) | threshold E | ΔVavg (kcal/mol) | σΔV (kcal/mol) | k0P |
| rex-GaMD | lower bound | 2.487 | 1.144 | vary |
| rex-GaMD | lower bound | 2.396 | 1.162 | vary |
| rex-GaMD | lower bound | 2.647 | 1.139 | vary |
| (C) | ||||
| σ0P (kcal/mol) | threshold E | ΔVavg (kcal/mol) | σΔV (kcal/mol) | k0P |
| 1.0 | rex-GaMD | 2.501 | 1.124 | vary |
| 1.0 | rex-GaMD | 2.690 | 1.097 | vary |
| 1.0 | rex-GaMD | 2.556 | 1.206 | vary |