3-pyridin-4-yl-2,4-dihydro-indeno[1,2-.c.]pyrazole Summary
TRAJECTORIES
METADATA
| Parameter | Value |
|---|---|
| Method | HamiltonianREMD |
| Number of MD replicas | 16 |
| Lenght 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 | 1579 |
| 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 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 | 0.86 | 0.87 | 0.87 | 0.87 | 0.88 | 0.88 | 0.88 |
| # Exchanges | 4262 | 4243 | 4279 | 4263 | 4298 | 4317 | 4304 | 4351 | 4343 | 4332 | 4354 | 4325 | 4363 | 4391 | 4423 |
| Avg. # Exchanges | 0.85 | 0.85 | 0.86 | 0.85 | 0.86 | 0.86 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 | 0.88 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 0.9030 | 0.5728 |
| RMSd_exp | - | - |
| RMSdist_first | 0.2955 | 0.1346 |
| RMSdist_exp | - | - |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 3.7141 | 0.0279 |
| RgyrX | 3.0847 | 0.0693 |
| RgyrY | 3.4654 | 0.0798 |
| RgyrZ | 2.4601 | 0.0475 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 0.7677 |
| Standard deviation (Å) | 0.4974 |
Atoms list
| Atom name | Fluctuation |
|---|---|
| O | 0.0363 |
| O1 | 0.0671 |
| O2 | 0.0506 |
| N | 0.1261 |
| C | 0.0119 |
| C1 | 0.1362 |
| C2 | 0.1383 |
| C3 | 0.1292 |
| C4 | 0.1374 |
| C5 | 0.134 |
| C6 | 0.1305 |
| C7 | 0.1404 |
| C8 | 0.1295 |
| C9 | 0.1337 |
| C10 | 0.0193 |
| C11 | 0.0347 |
| C12 | 0.0192 |
| C13 | 0.0444 |
| C14 | 0.0232 |
| C15 | 0.0719 |
| C16 | 0.0351 |
| C17 | 0.0366 |
| C18 | 0.0288 |
| C19 | 0.0281 |
3D View
Fluctuation Plot