13-cyclohexyl-3-methoxy-17,22-dimethyl-7h-10,6-(methanoiminothioiminobutanoiminomethano)indolo[2,1-a][2]benzazepine-14,23-dione 16,16-dioxide (0LN) 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 | 80 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 2498 |
| 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 | 0.81 | 0.82 | 0.82 | 0.82 | 0.82 | 0.83 | 0.82 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.85 | 0.84 |
| # Exchanges | 4026 | 4137 | 4117 | 4141 | 4089 | 4151 | 4097 | 4147 | 4158 | 4156 | 4206 | 4202 | 4248 | 4228 | 4173 |
| Avg. # Exchanges | 0.81 | 0.83 | 0.82 | 0.83 | 0.82 | 0.83 | 0.82 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.85 | 0.85 | 0.83 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.3058 | 0.1746 |
| RMSd_exp | 0.9745 | 0.1129 |
| RMSdist_first | 0.7830 | 0.0909 |
| RMSdist_exp | 0.5077 | 0.0630 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.9273 | 0.0552 |
| RgyrX | 4.0435 | 0.0498 |
| RgyrY | 4.7511 | 0.0658 |
| RgyrZ | 3.1035 | 0.0502 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 0.4028 |
| Standard deviation (Å) | 0.2204 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| O36 | 0.94 |
| C34 | 0.422 |
| N35 | 0.357 |
| C38 | 0.784 |
| C37 | 0.62 |
| C39 | 0.733 |
| C40 | 0.768 |
| C41 | 0.564 |
| N31 | 0.388 |
| C42 | 0.676 |
| S30 | 0.258 |
| O32 | 0.519 |
| O33 | 0.444 |
| N29 | 0.285 |
| C27 | 0.309 |
| O28 | 0.588 |
| C1 | 0.264 |
| C19 | 0.278 |
| C20 | 0.282 |
| N9 | 0.249 |
| C5 | 0.237 |
| C6 | 0.274 |
| C18 | 0.249 |
| C17 | 0.184 |
| C24 | 0.241 |
| C23 | 0.276 |
| O25 | 0.428 |
| C26 | 1.147 |
| C22 | 0.274 |
| C21 | 0.228 |
| C16 | 0.176 |
| C8 | 0.205 |
| C7 | 0.187 |
| C4 | 0.21 |
| C3 | 0.256 |
| C2 | 0.279 |
| C10 | 0.201 |
| C15 | 0.307 |
| C14 | 0.455 |
| C13 | 0.522 |
| C12 | 0.49 |
| C11 | 0.364 |
3D View
Fluctuation Plot