N-(2-aminoethyl)-5-(2-{[4-(morpholin-4-yl)pyridin-2-yl]amino}-1,3-thiazol-5-yl)pyridine-3-carboxamide (S25) 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 | 54 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 2532 |
| 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 | 0.80 | 0.80 | 0.81 | 0.81 | 0.81 | 0.82 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 |
| # Exchanges | 4019 | 4012 | 4056 | 4076 | 4106 | 4109 | 4100 | 4116 | 4130 | 4134 | 4140 | 4115 | 4178 | 4164 | 4219 |
| Avg. # Exchanges | 0.80 | 0.80 | 0.81 | 0.82 | 0.82 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.83 | 0.82 | 0.84 | 0.83 | 0.84 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.5320 | 0.4857 |
| RMSd_exp | 2.4591 | 0.4034 |
| RMSdist_first | 1.5212 | 0.5672 |
| RMSdist_exp | 1.3929 | 0.2597 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.1356 | 0.3283 |
| RgyrX | 2.6947 | 0.2053 |
| RgyrY | 4.7791 | 0.3285 |
| RgyrZ | 4.7388 | 0.5070 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.6181 |
| Standard deviation (Å) | 0.8148 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C | 1.82 |
| N | 1.01 |
| O | 2.373 |
| S | 0.838 |
| C1 | 2.347 |
| C2 | 2.373 |
| C3 | 1.853 |
| C4 | 1.156 |
| C5 | 0.548 |
| C6 | 0.849 |
| C7 | 2.011 |
| N8 | 2.815 |
| C9 | 2.367 |
| C10 | 1.002 |
| C11 | 0.947 |
| C12 | 1.529 |
| N13 | 1.664 |
| C14 | 1.219 |
| C15 | 1.72 |
| N16 | 1.577 |
| C17 | 0.905 |
| C18 | 0.512 |
| C19 | 0.616 |
| N20 | 1.18 |
| C21 | 0.827 |
| O22 | 1.254 |
| N23 | 1.594 |
| C24 | 2.541 |
| C25 | 3.355 |
| N26 | 3.741 |
3D View
Fluctuation Plot