O-methyl-n-[(2s)-4-methyl-2-(sulfanylmethyl)pentanoyl]-l-tyrosine (0QI) 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 | 47 |
| Molecule charge (simulated) | -1 |
| System number of atoms | 1853 |
| 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 | 0.83 | 0.83 | 0.83 | 0.84 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 | 0.84 | 0.85 | 0.85 |
| # Exchanges | 4127 | 4139 | 4186 | 4189 | 4118 | 4141 | 4156 | 4180 | 4184 | 4173 | 4216 | 4253 | 4246 | 4248 | 4224 |
| Avg. # Exchanges | 0.83 | 0.83 | 0.84 | 0.84 | 0.82 | 0.83 | 0.83 | 0.84 | 0.84 | 0.83 | 0.84 | 0.85 | 0.85 | 0.85 | 0.84 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.8249 | 0.4711 |
| RMSd_exp | 1.9012 | 0.5322 |
| RMSdist_first | 1.0253 | 0.2631 |
| RMSdist_exp | 1.0607 | 0.3239 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 3.9654 | 0.2873 |
| RgyrX | 3.5719 | 0.2375 |
| RgyrY | 3.0749 | 0.1320 |
| RgyrZ | 3.0259 | 0.4133 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.4204 |
| Standard deviation (Å) | 0.5002 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.638 |
| O1 | 1.014 |
| C2 | 0.724 |
| CH | 1.234 |
| S | 1.729 |
| C3 | 1.09 |
| C4 | 1.516 |
| CM | 2.282 |
| C5 | 2.095 |
| N | 0.701 |
| CA | 1.065 |
| C | 1.284 |
| O | 1.781 |
| CB | 1.651 |
| CG | 0.842 |
| CD1 | 1.332 |
| CD2 | 1.331 |
| CE1 | 1.46 |
| CE2 | 1.424 |
| CZ | 1.153 |
| OH | 1.931 |
| OXT | 1.802 |
| C6 | 2.591 |
3D View
Fluctuation Plot