N-[1h-indol-3-yl-acetyl]valine acid (IAV) 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 | 37 |
| Molecule charge (simulated) | -1 |
| System number of atoms | 1405 |
| 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 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 | 0.86 | 0.85 | 0.85 |
| # Exchanges | 4127 | 4137 | 4135 | 4133 | 4197 | 4197 | 4222 | 4237 | 4208 | 4205 | 4245 | 4252 | 4273 | 4222 | 4260 |
| Avg. # Exchanges | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.85 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.84 | 0.85 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.6540 | 0.4402 |
| RMSd_exp | 1.7980 | 0.4673 |
| RMSdist_first | 0.8670 | 0.2135 |
| RMSdist_exp | 0.9393 | 0.2740 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 3.5476 | 0.2145 |
| RgyrX | 2.4218 | 0.1361 |
| RgyrY | 2.8755 | 0.1879 |
| RgyrZ | 3.3180 | 0.2593 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.3542 |
| Standard deviation (Å) | 0.5141 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| O1 | 1.538 |
| C10 | 1.056 |
| N2 | 0.719 |
| C11 | 0.409 |
| C12 | 0.923 |
| O2 | 1.652 |
| O3 | 1.635 |
| C13 | 1.289 |
| C14 | 2.178 |
| C15 | 2.238 |
| C9 | 1.664 |
| C2 | 0.98 |
| C1 | 1.733 |
| N1 | 1.745 |
| C8 | 0.826 |
| C6 | 1.248 |
| C7 | 0.399 |
| C3 | 1.403 |
| C4 | 1.863 |
| C5 | 1.585 |
3D View
Fluctuation Plot