Table 1.
Breakdown of computational resources required in multicanonical simulations of wild type (WT) and mutant (MT) of MNK6, and of DS119. The resources for the initial replica exchange molecular dynamics run are listed under REMD.
| System | REMD | Pre-production | Production | Total |
|---|---|---|---|---|
| MNK6(WT) | 1400 ns (100 ns×14)1 | 300 ns (20 ns×5×3)2 | 250 ns (50 ns×5)3 | 900 ns |
| MNK6(MT) | 1400 ns (100 ns×14)1 | 300 ns (20 ns×5×3) | 250 ns (50 ns×5) | 900 ns |
| DS119 | 325 ns (25 ns×13) | 750 ns (50 ns×5×3) | 720 ns (120 ns×6) | 1795 ns |
1
The replica exchange run of Ref. 17 was used to prime the multicanonical simulation, hence, this is an overestimation of required resources.
2
simulation length of one multicanonical simulation × number of parallel runs × number of pre-production iterations
3
simulation length of one multicanonical simulation × number of production runs