Table 1.
The alchemical pathway for the first phase of the mutation. The angular and Van der Waals interactions between “P” and “M” particles are created, while torsions, improper torsions and electrostatic 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).
| MPH1 | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| scaling | correction | |||||||||
| P-P | P-M | P-N | M-M | N-N | P-P | P-M | P-N | M-M | N-N | |
| Vdw | 1 | λ4 | 1 | 1 | 1 | Soft core | ||||
| Ele | 1 | 0 | (1−λ) | 1 | 1 | |||||
| Bond | 1 | 1 | 1 | 1 | 1 | |||||
| Angle | 1 | λ2 | 1 | 1 | 1 | Urey-Bradley | ||||
| Tors | 1 | 0 | (1−λ)2 | 1 | 1 | |||||
| ImpT | 1 | 0 | (1−λ)2 | 1 | 1 | |||||