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 | 1873 |
| 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 | 0.85 | 0.86 | 0.85 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 | 0.87 | 0.88 |
| # Exchanges | 4267 | 4307 | 4270 | 4264 | 4333 | 4351 | 4369 | 4338 | 4320 | 4335 | 4394 | 4357 | 4352 | 4374 | 4375 |
| Avg. # Exchanges | 0.85 | 0.86 | 0.85 | 0.85 | 0.87 | 0.87 | 0.87 | 0.87 | 0.86 | 0.87 | 0.88 | 0.87 | 0.87 | 0.87 | 0.88 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.9722 | 0.4688 |
| RMSd_exp | 1.8242 | 0.3893 |
| RMSdist_first | 1.7226 | 0.5692 |
| RMSdist_exp | 1.3962 | 0.4448 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 3.6436 | 0.3765 |
| RgyrX | 2.4815 | 0.0761 |
| RgyrY | 3.0539 | 0.4836 |
| RgyrZ | 3.3104 | 0.3910 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.1390 |
| Standard deviation (Å) | 0.5723 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| CL | 1.5 |
| N1 | 1.104 |
| C1 | 1.23 |
| C2 | 0.941 |
| C3 | 0.522 |
| C4 | 0.433 |
| C5 | 0.777 |
| C6 | 1.066 |
| C7 | 1.012 |
| C8 | 0.876 |
| C9 | 0.686 |
| N2 | 0.704 |
| C10 | 0.688 |
| C11 | 0.901 |
| C12 | 0.971 |
| C13 | 0.91 |
| N3 | 0.936 |
| C14 | 1.694 |
| C15 | 2.609 |
| C16 | 1.775 |
| C17 | 2.646 |
| C18 | 1.077 |
3D View
Fluctuation Plot