R-3-fluoro-4-[2-hydroxy-2-(5,5,8,8-tetramethyl-5,6,7,8,-tetrahydro-naphtalen-2-yl)-acetylamino]-benzoic acid (394) 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 | 54 |
| Molecule charge (simulated) | -1 |
| System number of atoms | 2388 |
| 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 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.83 | 0.84 | 0.84 | 0.84 |
| # Exchanges | 4063 | 4100 | 4122 | 4121 | 4155 | 4092 | 4124 | 4180 | 4206 | 4189 | 4200 | 4154 | 4219 | 4199 | 4193 |
| Avg. # Exchanges | 0.81 | 0.82 | 0.82 | 0.82 | 0.83 | 0.82 | 0.82 | 0.84 | 0.84 | 0.84 | 0.84 | 0.83 | 0.84 | 0.84 | 0.84 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.0714 | 0.6467 |
| RMSd_exp | 2.0600 | 0.5649 |
| RMSdist_first | 1.2330 | 0.3116 |
| RMSdist_exp | 0.9039 | 0.2622 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.6554 | 0.2254 |
| RgyrX | 3.4295 | 0.1658 |
| RgyrY | 4.2017 | 0.2569 |
| RgyrZ | 3.7299 | 0.1615 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.3966 |
| Standard deviation (Å) | 0.6315 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 1.165 |
| C2 | 1.189 |
| C3 | 0.587 |
| C4 | 1.385 |
| C5 | 1.382 |
| C6 | 0.524 |
| C7 | 0.873 |
| C8 | 0.945 |
| C9 | 0.65 |
| C10 | 1.465 |
| C11 | 1.69 |
| C12 | 0.802 |
| C13 | 1.308 |
| C14 | 0.898 |
| C15 | 1.549 |
| C16 | 1.722 |
| C17 | 0.635 |
| C18 | 2.662 |
| C19 | 2.893 |
| C20 | 2.399 |
| C21 | 2.393 |
| C22 | 1.049 |
| C23 | 0.93 |
| N6 | 0.77 |
| F1 | 2.295 |
| O22 | 1.615 |
| O23 | 1.812 |
| O71 | 1.44 |
| O72 | 1.475 |
3D View
Fluctuation Plot