N4-(7-chloro-quinolin-4-yl)-n1,n1-diethyl-pentane-1,4-diamine (CLQ) 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 | 49 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 2350 |
| 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 | 0.86 | 0.86 | 0.85 | 0.86 | 0.86 | 0.86 | 0.87 | 0.86 | 0.87 | 0.87 | 0.87 | 0.88 | 0.88 | 0.88 | 0.88 |
| # Exchanges | 4264 | 4295 | 4271 | 4307 | 4310 | 4318 | 4328 | 4315 | 4370 | 4305 | 4403 | 4342 | 4385 | 4413 | 4403 |
| Avg. # Exchanges | 0.85 | 0.86 | 0.85 | 0.86 | 0.86 | 0.86 | 0.87 | 0.86 | 0.87 | 0.86 | 0.88 | 0.87 | 0.88 | 0.88 | 0.88 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.3086 | 0.5770 |
| RMSd_exp | 2.5531 | 0.5591 |
| RMSdist_first | 0.9939 | 0.5222 |
| RMSdist_exp | 2.2072 | 0.6856 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 3.6014 | 0.3824 |
| RgyrX | 2.5876 | 0.2074 |
| RgyrY | 3.1964 | 0.4758 |
| RgyrZ | 2.9966 | 0.2652 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.0669 |
| Standard deviation (Å) | 0.5893 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| CL | 1.414 |
| N1 | 0.876 |
| C1 | 0.932 |
| C2 | 0.756 |
| C3 | 0.491 |
| C4 | 0.447 |
| C5 | 0.662 |
| C6 | 0.919 |
| C7 | 0.97 |
| C8 | 0.857 |
| C9 | 0.638 |
| N2 | 0.644 |
| C10 | 0.614 |
| C11 | 0.864 |
| C12 | 0.92 |
| C13 | 0.876 |
| N3 | 0.953 |
| C14 | 1.741 |
| C15 | 2.612 |
| C16 | 1.766 |
| C17 | 2.609 |
| C18 | 0.911 |
3D View
Fluctuation Plot