Table 2.
Original and optimized Lennard-Jones parameters for RS-peptide.
| Original FF | Optimized FF | |||||
|---|---|---|---|---|---|---|
| Atom type | σ | ϵ | σ | ϵ | % Change σ | % Change ϵ |
| C | 0.339967 | 0.359824 | 0.339966 | 0.359787 | –0.000235359 | –0.0104181 |
| H | 0.106908 | 0.0656888 | 0.106908 | 0.0656513 | –0.000374220 | –0.0570937 |
| HB | 0.106908 | 0.0656888 | 0.106908 | 0.0657721 | –0.000374220 | 0.126688 |
| N | 0.325000 | 0.711280 | 0.325000 | 0.711355 | 0.000123099 | 0.0105384 |
| N3 | 0.325000 | 0.711280 | 0.324998 | 0.711156 | –0.000492395 | –0.0173983 |
| OB | 0.295992 | 0.878640 | 0.295992 | 0.878593 | –0.000135163 | –0.00539543 |
| O2 | 0.295992 | 0.8786401 | 0.295992 | 0.878633 | 0.000135163 | –0.000784472 |
| OW-tip4pd | 0.316500 | 0.998989 | 0.316502 | 0.998914 | 0.000505619 | –0.00750471 |
C, backbone carbonyl carbon; H, hydrogen bound to N-terminal nitrogen; HB, hydrogen bound to backbone amide nitrogen; N, backbone amide nitrogen; N3, N-terminal amine nitrogen; OB, backbone carbonyl oxygen; O2, C-terminal carboxyl oxygen; OW-tip4pd, water oxygen of TIP4P-d model.