Table 1.
Conformational diffusion constants and corresponding relaxation times (Eq. 1)
| Solvent simulation | Diffusion constant, nm2·ps−1 |
Relaxation time, ps |
Avg. H-bond lifetime, ps |
||||
|---|---|---|---|---|---|---|---|
| D0 | D∞ | τ1 | τ2 | τ3 | τwp | τpp | |
| Explicit | 0.02 (<0.01) | 2.6 (0.5) 10−5 | <1 | 7 (2) | 102 (5) | 8 (3) | 132 (21) |
| GB/SA | 0.05 (0.01) | 5.5 (0.5) 10−5 | <1 | — | 43 (4) | — | 49 (10) |
D0 is the short-time diffusion constant; D∞ is the long-time diffusion constant; and τ1, τ2, and τ3 are the relaxation times. The data are calculated over a time range of 1,000 ps and 500 ps for the explicit and implicit solvent simulations, respectively. In the last two columns are reported the average hydrogen bond lifetimes for two different kinds of hydrogen bonds: water–peptide, τwp, and intrapeptide, τpp. Noise is indicated in parentheses and corresponds to a standard deviation.