4-(n-hydroxyamino)-2r-isobutyl-2s-(2-thienylthiomethyl)succinyl-l-phenylalanine-n-methylamide (BAT) Summary
TRAJECTORIES
METADATA
| Parameter | Value |
|---|---|
| Method | HamiltonianREMD |
| Number of MD replicas | 16 |
| Length of the MD simulations (ns) | 10 |
| Number of steps between exchanges | 100 |
| Force Field | General Amber Force Field (GAFF) |
| Charge scheme | Semi-Empirical (AM1) |
| REMD Progression | Geometric Progression |
| Initial (low) temperature (K) / Scaling factor | 298 / 1 |
| Final (high) temperature (K) / Scaling factor | 498 / 0.59 |
| Molecule number of atoms | 63 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 2181 |
| Box size in simulations (nm) | 0.8 |
| Solvent model | TIP3P |
| Box type in simulations | Octahedron |
| MD ensemble | NVT |
REMD stats
| 1-2 | 2-3 | 3-4 | 4-5 | 5-6 | 6-7 | 7-8 | 8-9 | 9-10 | 10-11 | 11-12 | 12-13 | 13-14 | 14-15 | 15-16 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Probabilities | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 | 0.85 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 |
| # Exchanges | 4225 | 4212 | 4170 | 4229 | 4213 | 4246 | 4210 | 4247 | 4254 | 4275 | 4226 | 4217 | 4246 | 4261 | 4258 |
| Avg. # Exchanges | 0.85 | 0.84 | 0.83 | 0.85 | 0.84 | 0.85 | 0.84 | 0.85 | 0.85 | 0.86 | 0.85 | 0.84 | 0.85 | 0.85 | 0.85 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.2872 | 0.8495 |
| RMSd_exp | 2.3110 | 0.4782 |
| RMSdist_first | 1.2301 | 0.3110 |
| RMSdist_exp | 1.2574 | 0.3733 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.1756 | 0.2180 |
| RgyrX | 3.7323 | 0.3005 |
| RgyrY | 3.3889 | 0.3413 |
| RgyrZ | 3.0505 | 0.1985 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.7697 |
| Standard deviation (Å) | 0.8277 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.917 |
| C2 | 1.766 |
| C3 | 1.046 |
| C4 | 1.39 |
| C5 | 2.029 |
| C6 | 2.724 |
| C7 | 3.033 |
| C8 | 0.701 |
| C9 | 1.112 |
| C10 | 1.528 |
| C11 | 1.88 |
| C12 | 2.172 |
| C13 | 0.53 |
| C14 | 0.79 |
| C15 | 0.996 |
| C16 | 1.812 |
| C17 | 1.267 |
| C18 | 1.355 |
| C19 | 2.112 |
| C20 | 2.928 |
| C21 | 3.164 |
| C22 | 2.897 |
| C23 | 2.086 |
| N1 | 2.63 |
| N2 | 0.539 |
| N3 | 1.244 |
| O1 | 2.267 |
| O2 | 3.68 |
| O3 | 0.91 |
| O4 | 1.411 |
| S1 | 1.337 |
| S2 | 2.379 |
3D View
Fluctuation Plot