1,3-bis-(4-methoxy-benzenesulfonyl)-5,5-dimethyl-hexahydro-pyrimidine-2-carboxylic acid hydroxyamide (N25) 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 | 61 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1708 |
| 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 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.85 | 0.84 | 0.85 | 0.85 | 0.86 | 0.85 | 0.86 | 0.86 | 0.86 |
| # Exchanges | 4140 | 4115 | 4158 | 4198 | 4157 | 4226 | 4218 | 4220 | 4254 | 4286 | 4277 | 4247 | 4293 | 4292 | 4334 |
| Avg. # Exchanges | 0.83 | 0.82 | 0.83 | 0.84 | 0.83 | 0.85 | 0.84 | 0.84 | 0.85 | 0.86 | 0.86 | 0.85 | 0.86 | 0.86 | 0.87 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.2141 | 0.5744 |
| RMSd_exp | 3.0659 | 0.1265 |
| RMSdist_first | 0.6862 | 0.3465 |
| RMSdist_exp | 1.3038 | 0.1393 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.3785 | 0.1803 |
| RgyrX | 2.7625 | 0.1437 |
| RgyrY | 3.8075 | 0.3258 |
| RgyrZ | 4.0139 | 0.1992 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.1016 |
| Standard deviation (Å) | 0.4110 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.471 |
| C2 | 1.228 |
| C3 | 1.349 |
| C4 | 0.983 |
| C5 | 1.409 |
| C6 | 1.257 |
| O7 | 1.392 |
| C8 | 1.888 |
| N9 | 0.495 |
| S10 | 0.728 |
| O11 | 1.198 |
| O12 | 1.129 |
| C13 | 0.341 |
| N14 | 0.544 |
| C15 | 0.808 |
| C16 | 1.041 |
| C17 | 0.768 |
| C18 | 1.527 |
| C19 | 1.351 |
| S20 | 0.777 |
| O21 | 1.213 |
| O22 | 1.282 |
| C23 | 0.486 |
| N25 | 0.816 |
| C27 | 0.463 |
| C28 | 1.323 |
| C29 | 1.499 |
| C30 | 1.092 |
| C31 | 1.468 |
| C32 | 1.305 |
| O33 | 1.56 |
| C34 | 2.081 |
| O24 | 1.015 |
| O26 | 1.166 |
3D View
Fluctuation Plot