4-[3-oxo-3-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-naphthalen-2-yl)-propenyl]-benzoic acid (156) 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 | 52 |
| Molecule charge (simulated) | -1 |
| System number of atoms | 2224 |
| 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 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 |
| # Exchanges | 4124 | 4136 | 4171 | 4167 | 4185 | 4128 | 4145 | 4168 | 4219 | 4244 | 4244 | 4275 | 4208 | 4235 | 4288 |
| Avg. # Exchanges | 0.82 | 0.83 | 0.83 | 0.83 | 0.84 | 0.83 | 0.83 | 0.83 | 0.84 | 0.85 | 0.85 | 0.86 | 0.84 | 0.85 | 0.86 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.1542 | 0.6240 |
| RMSd_exp | 1.2075 | 0.6289 |
| RMSdist_first | 0.6262 | 0.3924 |
| RMSdist_exp | 0.6301 | 0.4049 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.7811 | 0.1637 |
| RgyrX | 4.0709 | 0.2901 |
| RgyrY | 4.5815 | 0.1253 |
| RgyrZ | 2.8474 | 0.0449 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 0.8952 |
| Standard deviation (Å) | 0.5180 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.633 |
| C2 | 0.418 |
| C3 | 0.535 |
| C4 | 0.46 |
| C5 | 0.306 |
| C8 | 0.444 |
| C9 | 0.619 |
| C6 | 0.324 |
| C7 | 0.333 |
| C10 | 0.814 |
| C11 | 0.652 |
| C12 | 0.51 |
| C13 | 0.451 |
| C14 | 1.373 |
| C15 | 1.385 |
| C16 | 0.636 |
| C17 | 0.536 |
| C18 | 0.462 |
| C19 | 1.282 |
| C20 | 1.336 |
| C21 | 2.074 |
| C22 | 2.141 |
| C23 | 1.335 |
| C24 | 1.392 |
| O1 | 1.272 |
| O2 | 1.3 |
| O3 | 1.148 |
3D View
Fluctuation Plot