Table 4. Restraints used during energy minimization (EM) and stepwise equilibration (steps 1–6) of the asymmetric plasma membrane mimetic in kJ mol-1nm-2.
Step | Time [ns] | Timestep [fs] | Ensemble | Lipids | Dihedrals |
---|---|---|---|---|---|
EM | 1000 | 1000 | |||
1 | 0.125 | 1 | NVT | 1000 | 1000 |
2 | 0.125 | 1 | NVT | 400 | 400 |
3 | 0.125 | 1 | NPT | 400 | 200 |
4 | 0.5 | 2 | NPT | 200 | 200 |
5 | 0.5 | 2 | NPT | 40 | 100 |
6 | 0.5 | 2 | NPT | 0 | 0 |