N-[2-(4-bromocinnamylamino)ethyl]-5-isoquinoline sulfonamide (IQB) 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) | 1 |
| System number of atoms | 2112 |
| 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 | 0.81 | 0.81 | 0.81 | 0.81 | 0.82 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 |
| # Exchanges | 3999 | 4060 | 4029 | 4053 | 4184 | 4105 | 4196 | 4198 | 4227 | 4157 | 4199 | 4247 | 4218 | 4226 | 4313 |
| Avg. # Exchanges | 0.80 | 0.81 | 0.81 | 0.81 | 0.84 | 0.82 | 0.84 | 0.84 | 0.85 | 0.83 | 0.84 | 0.85 | 0.84 | 0.85 | 0.86 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.6274 | 0.6483 |
| RMSd_exp | 2.7214 | 0.3727 |
| RMSdist_first | 2.0915 | 0.7470 |
| RMSdist_exp | 1.8142 | 0.3788 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.5171 | 0.5416 |
| RgyrX | 4.1827 | 0.6162 |
| RgyrY | 3.3728 | 0.3958 |
| RgyrZ | 3.4413 | 0.3815 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.8940 |
| Standard deviation (Å) | 0.5716 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.925 |
| C2 | 2.08 |
| C3 | 2.682 |
| C4 | 2.355 |
| C5 | 1.705 |
| C6 | 2.425 |
| N7 | 3.015 |
| C8 | 2.883 |
| C9 | 1.884 |
| C10 | 1.06 |
| S | 1.166 |
| O1 | 1.843 |
| O2 | 1.841 |
| N1' | 1.102 |
| C2' | 1.664 |
| C3' | 1.985 |
| N4' | 1.8 |
| C5' | 2.152 |
| C6' | 1.529 |
| C7' | 1.344 |
| C1' | 1.123 |
| C2B | 1.499 |
| C3B | 2.008 |
| C4' | 2.023 |
| BR4' | 2.98 |
| C5B | 2.162 |
| C6B | 1.903 |
3D View
Fluctuation Plot