1-benzyl-4-[(5,6-dimethoxy-1-indanon-2-yl)methyl]piperidine (E20) 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 | 58 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 2779 |
| 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 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 | 0.88 | 0.88 | 0.88 |
| # Exchanges | 4259 | 4296 | 4302 | 4320 | 4268 | 4317 | 4333 | 4372 | 4325 | 4356 | 4351 | 4410 | 4395 | 4379 | 4402 |
| Avg. # Exchanges | 0.85 | 0.86 | 0.86 | 0.86 | 0.85 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 | 0.88 | 0.88 | 0.88 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.4393 | 0.4556 |
| RMSd_exp | 1.6235 | 0.4104 |
| RMSdist_first | 0.4818 | 0.2384 |
| RMSdist_exp | 0.5823 | 0.1459 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.4027 | 0.1643 |
| RgyrX | 5.2490 | 0.1778 |
| RgyrY | 1.6625 | 0.1586 |
| RgyrZ | 5.2926 | 0.2172 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.1727 |
| Standard deviation (Å) | 0.4243 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.645 |
| C2 | 0.535 |
| C3 | 0.883 |
| C4 | 0.668 |
| C5 | 0.452 |
| C6 | 0.813 |
| C7 | 0.778 |
| C8 | 0.924 |
| C9 | 1.206 |
| C10 | 1.18 |
| C11 | 0.814 |
| C12 | 1.374 |
| C13 | 1.408 |
| N14 | 0.962 |
| C15 | 1.531 |
| C16 | 1.493 |
| C17 | 1.394 |
| C18 | 0.588 |
| C19 | 1.345 |
| C20 | 1.814 |
| C21 | 1.847 |
| C22 | 1.849 |
| C23 | 1.36 |
| O24 | 1.281 |
| O25 | 1.218 |
| C26 | 1.967 |
| O27 | 0.928 |
| C28 | 1.58 |
3D View
Fluctuation Plot