6-[hydroxy-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-naphtalen-2-yl)-methyl]-naphtalene-2-carboxylic acid (184) 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 | 56 |
| Molecule charge (simulated) | -1 |
| System number of atoms | 2372 |
| 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 | 0.82 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 |
| # Exchanges | 4136 | 4130 | 4093 | 4140 | 4168 | 4164 | 4232 | 4226 | 4186 | 4221 | 4225 | 4204 | 4238 | 4243 | 4276 |
| Avg. # Exchanges | 0.83 | 0.83 | 0.82 | 0.83 | 0.83 | 0.83 | 0.85 | 0.85 | 0.84 | 0.84 | 0.85 | 0.84 | 0.85 | 0.85 | 0.86 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.7414 | 0.7055 |
| RMSd_exp | 1.8867 | 0.5700 |
| RMSdist_first | 0.5770 | 0.1577 |
| RMSdist_exp | 0.8237 | 0.2919 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.6593 | 0.1489 |
| RgyrX | 3.9908 | 0.1508 |
| RgyrY | 2.8329 | 0.0747 |
| RgyrZ | 4.4112 | 0.1529 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.3580 |
| Standard deviation (Å) | 0.6117 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.886 |
| C2 | 0.553 |
| C3 | 1.496 |
| C4 | 1.737 |
| C5 | 0.787 |
| C10 | 0.599 |
| C11 | 0.907 |
| C15 | 0.515 |
| C16 | 1.761 |
| C17 | 1.679 |
| C18 | 1.021 |
| C19 | 1.012 |
| C20 | 0.762 |
| C23 | 2.728 |
| C24 | 2.891 |
| C25 | 2.288 |
| C26 | 1.823 |
| O1 | 1.449 |
| O2 | 1.531 |
| C6 | 1.157 |
| C7 | 0.75 |
| C8 | 1.405 |
| C9 | 1.58 |
| C13 | 0.889 |
| C14 | 0.662 |
| C21 | 1.852 |
| C22 | 1.86 |
| C12 | 1.142 |
| O3 | 1.66 |
3D View
Fluctuation Plot