2-(2-chloro-phenyl)-5,7-dihydroxy-8-(3-hydroxy-1-methyl-piperidin-4-yl)-4h-benzopyran-4-one (CPB) 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 | 1573 |
| 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 | 0.84 | 0.84 | 0.84 | 0.84 | 0.85 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.85 | 0.86 | 0.87 |
| # Exchanges | 4174 | 4198 | 4198 | 4262 | 4306 | 4218 | 4230 | 4268 | 4229 | 4272 | 4351 | 4253 | 4275 | 4306 | 4271 |
| Avg. # Exchanges | 0.83 | 0.84 | 0.84 | 0.85 | 0.86 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.87 | 0.85 | 0.86 | 0.86 | 0.85 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 0.7470 | 0.2495 |
| RMSd_exp | 0.5891 | 0.2623 |
| RMSdist_first | 0.4628 | 0.1862 |
| RMSdist_exp | 0.3638 | 0.1836 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 3.8917 | 0.0407 |
| RgyrX | 3.6995 | 0.0600 |
| RgyrY | 2.9894 | 0.0497 |
| RgyrZ | 2.7685 | 0.0229 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 0.3632 |
| Standard deviation (Å) | 0.2870 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.434 |
| N1 | 0.252 |
| C16 | 0.354 |
| C15 | 0.299 |
| C14 | 0.175 |
| C13 | 0.261 |
| C12 | 0.28 |
| C8 | 0.148 |
| C9 | 0.164 |
| O1 | 0.276 |
| C2 | 0.203 |
| C3 | 0.232 |
| C4 | 0.219 |
| O4 | 0.326 |
| C10 | 0.138 |
| C5 | 0.139 |
| O5 | 0.235 |
| C6 | 0.202 |
| C7 | 0.188 |
| O7 | 0.314 |
| C21 | 0.155 |
| C22 | 0.611 |
| CL1 | 1.487 |
| C23 | 0.625 |
| C24 | 0.378 |
| C25 | 0.87 |
| C26 | 0.813 |
| O3 | 0.392 |
3D View
Fluctuation Plot