4-(3,3-diphenylpropylamino)cinnoline-3-carbonitrile (MQ0) 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 | 48 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1866 |
| 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 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 | 0.88 | 0.88 | 0.88 | 0.88 | 0.88 | 0.89 | 0.88 | 0.89 | 0.89 | 0.89 |
| # Exchanges | 4343 | 4339 | 4368 | 4322 | 4402 | 4413 | 4393 | 4454 | 4408 | 4413 | 4406 | 4462 | 4463 | 4424 | 4480 |
| Avg. # Exchanges | 0.87 | 0.87 | 0.87 | 0.86 | 0.88 | 0.88 | 0.88 | 0.89 | 0.88 | 0.88 | 0.88 | 0.89 | 0.89 | 0.88 | 0.90 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.5701 | 0.6461 |
| RMSd_exp | 2.5490 | 0.5219 |
| RMSdist_first | 1.5218 | 0.3767 |
| RMSdist_exp | 1.5232 | 0.3925 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.0892 | 0.2481 |
| RgyrX | 3.7741 | 0.3291 |
| RgyrY | 3.5593 | 0.3435 |
| RgyrZ | 2.5269 | 0.2056 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.8713 |
| Standard deviation (Å) | 0.7066 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 1.974 |
| C2 | 2.777 |
| C3 | 2.748 |
| C4 | 2.061 |
| C5 | 1.178 |
| N6 | 1.459 |
| N7 | 1.609 |
| C8 | 1.196 |
| C9 | 0.584 |
| C10 | 0.914 |
| N11 | 1.341 |
| C12 | 1.45 |
| C13 | 1.329 |
| C16 | 0.959 |
| C15 | 0.793 |
| C17 | 1.793 |
| C18 | 2.55 |
| C19 | 2.75 |
| C20 | 2.138 |
| N19 | 2.933 |
| C21 | 2.593 |
| C22 | 1.842 |
| C23 | 1.186 |
| C24 | 1.948 |
| C25 | 2.668 |
| C26 | 2.87 |
| C27 | 2.743 |
| C28 | 2.011 |
3D View
Fluctuation Plot