Table 2.
The alchemical pathway for the second phase of the mutation. The torsions, improper torsions and electrostatic interactions between “P” and “M” particles are created, while angular and Van der Waals interactions between “P” and “N” are progressively switched off. The right hand side of the table reports the corrections to the regular OPLS-AAL26 potential that were used. Notice that the self-interactions, as well as the bonds, are never scaled (see details in the text).
| MPH2 | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| scaling | correction | |||||||||
| P-P | P-M | P-N | M-M | N-N | P-P | P-M | P-N | M-M | N-N | |
| Vdw | 1 | 1 | (1−λ)4 | 1 | 1 | Soft core | ||||
| Ele | 1 | λ | 0 | 1 | 1 | |||||
| Bond | 1 | 1 | 1 | 1 | 1 | |||||
| Angle | 1 | 1 | (1−λ)2 | 1 | 1 | Urey-Bradley | ||||
| Tors | 1 | λ2 | 0 | 1 | 1 | |||||
| ImpT | 1 | λ2 | 0 | 1 | 1 | |||||