Table 1.
Parameters for minimizing, equilibrating, and simulating 3D structures of characterised class C GH9 endoglucanases
| Min_1 | Min_2 | Equil_1 | Equil_2 | 40.1 ns | ||
|---|---|---|---|---|---|---|
| Algorithm | SD | SD | Shake | Shake | ||
| imin | 1 | 1 | 0 | 0 | 0 | |
| irest | 0 | 0 | 0 | 1 | – | |
| maxcyc | 5000 | 5000 | – | – | – | |
| ncyc | 10000 | 10000 | – | – | – | |
| ntc | – | – | 2.0 | 2.0 | – | |
| ntf | – | – | 2.0 | 2.0 | – | |
| ntr | 1 | 0 | 1 | 0 | – | |
| Force (Kcal mol−1) Ang2) | 100.0 | – | 10.0 | – | – | |
| ntt | – | – | 3.0 | 3.0 | – | |
| tempi (K) | – | – | 0 | 300.0 | 300.0 | |
| temp0 (K) | – | – | 300.0 | 300.0 | 300.0 | |
| igb | 0 | 0 | 0 | 0 | – | |
| cut (Ang) | 12.0 | 12.0 | 10.0 | 10.0 | 10.0 | |
| nstlim | 10000 | 50000 | 20,050,000 | |||
| dt | 0.002 | 0.002 | 0.002 | |||
| ntb | – | – | 1 | 2 | – | |
| ntp | – | – | 0.0 | 1.0 | – | |
| pres0 | – | – | – | 1.0 | ||
| taup | – | – | – | 2.0 | ||
| ntpr | 100 | 100 | 1000 | 10000 | 10000 | |
| ntwx | – | – | 1000 | 10000 | 10000 | |
| ntwr | – | – | 5000 | 10000 | 10000 | |
| Dielectric | – | – | – | – | 1.0 | |
| Simulation space partitioning | Switching | – | – | – | – | On |
| Switchdist (Ang) | 9 | |||||
| Pairlistdist (Ang) | 12 | |||||
| exclude | Scaled 1–4 | |||||
| 1–4scaling | 1.0 | |||||
| firsttimestep | Timestep | – | – | – | – | 1 |
| Stepspercycle | 20 | |||||
| nonbondedFreq | 2 | |||||
| fullElectFrequency | 4 | |||||
| Langevin dynamics | Langevin | – | – | – | – | On |
| LangevinDamping | 1.0 | |||||
| LangevinTemp | 300 | |||||
| LangevinHydrogen | No | |||||
| LangevinPiston | On | |||||
| LangevinPistonTarget | 1.01325 | |||||
| LangevinPistonPeriod | 2000 fs | |||||
| LangevinPistonDecay | 1000 fs | |||||
| LangevinPistonTemp | 300 | |||||
| useFlexibleCell | No | |||||
| useGroupPressure | No | |||||
| fixedAtomsForces | Off | |||||
| Cell basis vectors | CellBasisVector1 | – | – | – | – | x-coord,0,0 |
| CellBasisVector2 | 0,y-coord,0 | |||||
| CellBasisVector3 | 0,0,z-coord | |||||
| wrapAll | – | – | – | – | No | |
| dcdUnitCell | Yes | |||||