Table 1.
Steps | Timestep | Harmonic Constraints (kcal/mol/Å2) | |||||||
---|---|---|---|---|---|---|---|---|---|
Numstep | Temperature | Backbone | Ligand | Side Chains | Lipids | Water and Ions | Temperature Control | ||
Heating | |||||||||
1 | 2.0 fs | 100 ps | 300 K | 50 | 50 | 50 | 50 | 50 | NVT |
Equilibration Steps | |||||||||
2 | 2.0 fs | 100 ps | 300 K | 50 | 50 | 50 | 50 | 50 | NPT |
3 | 2.0 fs | 100 ps | 300 K | 50 | 50 | 50 | 50 | 10 | NPT |
4 | 2.0 fs | 100 ps | 300 K | 50 | 50 | 10 | 10 | 5 | NPT |
5 | 2.0 fs | 100 ps | 300 K | 50 | 10 | 5 | 5 | 1 | NPT |
6 | 2.0 fs | 100 ps | 300 K | 50 | 5 | 1 | 1 | - | NPT |
7 | 2.0 fs | 100 ps | 300 K | 25 | - | - | - | - | NPT |
8 | 2.0 fs | 100 ps | 300 K | 10 | - | - | - | - | NPT |
9 | 2.0 fs | 100 ps | 300 K | 5 | - | - | - | - | NPT |
10 | 2.0 fs | 250 ps | 300 K | 1 | - | - | - | - | NPT |
Production Run | |||||||||
11 | 2.0 fs | 20 ns | 300 K | - | - | - | - | - | NPT P=1.0132 bar T = 300 K |