N-hydroxy-2-[4-(4-phenoxy-benzenesulfonyl)-tetrahydro-pyran-4-yl]-acetamide (RS2) 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 | 48 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1962 |
| 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 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 |
| # Exchanges | 4246 | 4316 | 4276 | 4314 | 4323 | 4287 | 4364 | 4326 | 4321 | 4350 | 4339 | 4358 | 4413 | 4333 | 4343 |
| Avg. # Exchanges | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 | 0.87 | 0.86 | 0.87 | 0.87 | 0.87 | 0.88 | 0.87 | 0.87 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.3861 | 0.5408 |
| RMSd_exp | 2.2984 | 0.4782 |
| RMSdist_first | 1.3637 | 0.3160 |
| RMSdist_exp | 1.2348 | 0.2933 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.2827 | 0.1303 |
| RgyrX | 4.0666 | 0.2179 |
| RgyrY | 3.9152 | 0.1665 |
| RgyrZ | 2.1746 | 0.2191 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.2592 |
| Standard deviation (Å) | 0.4434 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 1.833 |
| C2 | 1.865 |
| C3 | 1.87 |
| C4 | 1.376 |
| C5 | 0.525 |
| C6 | 1.33 |
| O12 | 1.222 |
| C13 | 0.941 |
| C14 | 1.182 |
| C15 | 1.094 |
| C16 | 0.718 |
| C17 | 1.054 |
| C18 | 1.126 |
| S23 | 0.887 |
| C24 | 0.448 |
| O25 | 1.33 |
| O26 | 1.333 |
| C27 | 0.936 |
| C28 | 1.224 |
| O31 | 1.905 |
| N32 | 1.819 |
| O33 | 2.438 |
| C36 | 1.099 |
| C37 | 1.231 |
| O38 | 1.199 |
| C39 | 1.034 |
| C40 | 0.979 |
3D View
Fluctuation Plot