(1s,2s,5s)2-(4-glutaridylbenzyl)-5-phenyl-1-cyclohexanol (HOP) 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 | 2979 |
| 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 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.82 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 | 0.85 |
| # Exchanges | 4126 | 4100 | 4060 | 4107 | 4162 | 4108 | 4097 | 4163 | 4174 | 4174 | 4174 | 4185 | 4181 | 4234 | 4214 |
| Avg. # Exchanges | 0.83 | 0.82 | 0.81 | 0.82 | 0.83 | 0.82 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.85 | 0.84 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.5688 | 0.3212 |
| RMSd_exp | 1.6707 | 0.3633 |
| RMSdist_first | 0.7043 | 0.3581 |
| RMSdist_exp | 0.8135 | 0.2161 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.6134 | 0.2548 |
| RgyrX | 3.5195 | 0.1446 |
| RgyrY | 4.8159 | 0.1892 |
| RgyrZ | 5.2374 | 0.2882 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.2283 |
| Standard deviation (Å) | 0.4812 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.859 |
| C2 | 1.486 |
| C6 | 1.367 |
| C5 | 1.323 |
| C4 | 0.623 |
| C3 | 1.407 |
| C7 | 0.616 |
| C12 | 1.158 |
| C11 | 1.219 |
| C10 | 0.738 |
| C9 | 1.365 |
| C8 | 1.403 |
| C13 | 0.71 |
| C14 | 1.746 |
| C15 | 1.722 |
| C16 | 0.723 |
| C17 | 0.891 |
| C18 | 0.825 |
| O19 | 2.437 |
| C20 | 0.788 |
| O21 | 1.394 |
| N22 | 0.715 |
| C23 | 0.805 |
| C24 | 1.054 |
| C25 | 1.238 |
| C26 | 1.516 |
| O27 | 2.13 |
| O28 | 2.134 |
3D View
Fluctuation Plot