N-[1h-indol-3-yl-acetyl]glycine acid (IAG) 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 | 28 |
| Molecule charge (simulated) | -1 |
| System number of atoms | 1267 |
| 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 | 0.83 | 0.84 | 0.84 | 0.85 | 0.85 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 |
| # Exchanges | 4179 | 4126 | 4193 | 4184 | 4223 | 4275 | 4225 | 4193 | 4244 | 4240 | 4270 | 4275 | 4268 | 4277 | 4270 |
| Avg. # Exchanges | 0.84 | 0.83 | 0.84 | 0.84 | 0.84 | 0.86 | 0.85 | 0.84 | 0.85 | 0.85 | 0.85 | 0.86 | 0.85 | 0.86 | 0.85 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.7105 | 0.4128 |
| RMSd_exp | 1.5501 | 0.4222 |
| RMSdist_first | 0.8815 | 0.2590 |
| RMSdist_exp | 0.7341 | 0.2199 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 3.4258 | 0.2158 |
| RgyrX | 2.8787 | 0.2164 |
| RgyrY | 2.6864 | 0.1734 |
| RgyrZ | 2.8207 | 0.1680 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.0940 |
| Standard deviation (Å) | 0.3839 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| O3 | 1.54 |
| C12 | 0.794 |
| O2 | 1.511 |
| C11 | 0.747 |
| N2 | 0.564 |
| C10 | 0.979 |
| O1 | 1.841 |
| C9 | 1.368 |
| C2 | 0.699 |
| C1 | 1.239 |
| N1 | 1.479 |
| C7 | 0.416 |
| C8 | 0.754 |
| C6 | 1.058 |
| C5 | 1.024 |
| C4 | 1.359 |
| C3 | 1.226 |
3D View
Fluctuation Plot