(4-benzyl-piperidin-1-yl)-(5-amidinomethyl-3ah-indol-2-yl-methanone (BPP) 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 | 51 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 2286 |
| 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 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 | 0.86 | 0.87 | 0.87 |
| # Exchanges | 4217 | 4207 | 4267 | 4252 | 4245 | 4227 | 4307 | 4335 | 4315 | 4330 | 4311 | 4357 | 4330 | 4353 | 4382 |
| Avg. # Exchanges | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.87 | 0.86 | 0.87 | 0.86 | 0.87 | 0.87 | 0.87 | 0.88 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.5724 | 0.4463 |
| RMSd_exp | 2.0901 | 0.4979 |
| RMSdist_first | 0.6302 | 0.2895 |
| RMSdist_exp | 1.1908 | 0.2579 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.0912 | 0.1906 |
| RgyrX | 3.2993 | 0.0888 |
| RgyrY | 4.1356 | 0.1613 |
| RgyrZ | 4.8813 | 0.2536 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.2186 |
| Standard deviation (Å) | 0.4282 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.483 |
| C2 | 0.928 |
| C3 | 0.57 |
| C4 | 0.831 |
| C5 | 1.787 |
| C6 | 1.483 |
| C10 | 1.318 |
| C11 | 0.629 |
| N12 | 0.977 |
| C13 | 0.747 |
| N14 | 1.139 |
| N15 | 1.597 |
| C17 | 1.02 |
| O18 | 1.963 |
| N19 | 0.705 |
| C20 | 1.553 |
| C21 | 1.515 |
| C22 | 0.961 |
| C23 | 1.384 |
| C24 | 1.361 |
| C33 | 1.336 |
| C35 | 0.583 |
| C38 | 1.401 |
| C39 | 1.842 |
| C40 | 1.758 |
| C41 | 1.733 |
| C42 | 1.299 |
3D View
Fluctuation Plot