1,3-diphenyl-1-propyl-1-(3,3-dimethyl-1,2-dioxypentyl)-2-piperidine carboxylate (SB3) 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 | 68 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1880 |
| 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 | 0.86 | 0.87 | 0.86 | 0.86 | 0.87 | 0.86 | 0.87 | 0.87 | 0.87 | 0.88 | 0.88 | 0.88 | 0.88 | 0.88 |
| # Exchanges | 4297 | 4263 | 4337 | 4336 | 4305 | 4367 | 4322 | 4350 | 4341 | 4354 | 4368 | 4365 | 4396 | 4364 | 4391 |
| Avg. # Exchanges | 0.86 | 0.85 | 0.87 | 0.87 | 0.86 | 0.87 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 | 0.87 | 0.88 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.9646 | 0.6032 |
| RMSd_exp | 2.1155 | 0.5636 |
| RMSdist_first | 1.1382 | 0.2859 |
| RMSdist_exp | 1.2528 | 0.2870 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.3118 | 0.2695 |
| RgyrX | 3.4067 | 0.1953 |
| RgyrY | 3.4574 | 0.2156 |
| RgyrZ | 3.6860 | 0.3141 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.6543 |
| Standard deviation (Å) | 0.6379 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.972 |
| C2 | 1.065 |
| C3 | 1.722 |
| C4 | 1.915 |
| C5 | 1.71 |
| C6 | 1.108 |
| N7 | 0.624 |
| O1 | 1.225 |
| O2 | 0.98 |
| C8 | 0.65 |
| O3 | 1.249 |
| C9 | 0.867 |
| O4 | 1.115 |
| C10 | 1.57 |
| C11 | 2.27 |
| C12 | 2.952 |
| C13 | 2.47 |
| C14 | 2.322 |
| C15 | 1.007 |
| C16 | 1.3 |
| C17 | 1.328 |
| C18 | 1.071 |
| C19 | 1.851 |
| C20 | 2.6 |
| C21 | 2.792 |
| C22 | 2.556 |
| C23 | 1.796 |
| C24 | 1.198 |
| C25 | 1.811 |
| C26 | 2.209 |
| C27 | 2.182 |
| C28 | 2.261 |
| C29 | 1.845 |
3D View
Fluctuation Plot