2-hydroxy-(5-([4-(2-pyridinylamino)sulfonyl]phenyl)azo)benzoic acid (SAS) 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 | 41 |
| Molecule charge (simulated) | -1 |
| System number of atoms | 2000 |
| 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 | 0.79 | 0.79 | 0.80 | 0.81 | 0.81 | 0.81 | 0.82 | 0.82 | 0.83 | 0.83 | 0.84 | 0.83 | 0.84 | 0.84 | 0.84 |
| # Exchanges | 3956 | 3957 | 4037 | 4020 | 4048 | 4076 | 4102 | 4126 | 4108 | 4154 | 4214 | 4177 | 4212 | 4165 | 4191 |
| Avg. # Exchanges | 0.79 | 0.79 | 0.81 | 0.80 | 0.81 | 0.82 | 0.82 | 0.83 | 0.82 | 0.83 | 0.84 | 0.84 | 0.84 | 0.83 | 0.84 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.6894 | 0.4310 |
| RMSd_exp | 1.7289 | 0.4082 |
| RMSdist_first | 0.8541 | 0.2743 |
| RMSdist_exp | 0.9247 | 0.2573 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.0765 | 0.2648 |
| RgyrX | 4.1891 | 0.3135 |
| RgyrY | 4.7613 | 0.2993 |
| RgyrZ | 3.3574 | 0.0513 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.2808 |
| Standard deviation (Å) | 0.5649 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.612 |
| C2 | 1.475 |
| C3 | 2.108 |
| C4 | 2.121 |
| C5 | 1.976 |
| N1 | 1.44 |
| N2 | 0.765 |
| S1 | 0.651 |
| O1 | 1.106 |
| O2 | 1.071 |
| C6 | 0.5 |
| C7 | 1.312 |
| C8 | 1.332 |
| C9 | 0.646 |
| C10 | 1.33 |
| C11 | 1.295 |
| N3 | 0.832 |
| N4 | 0.856 |
| C12 | 0.82 |
| C13 | 0.649 |
| C14 | 0.512 |
| C15 | 1.036 |
| C16 | 2.071 |
| C17 | 1.935 |
| C18 | 1.568 |
| O3 | 1.276 |
| O4 | 2.24 |
| O5 | 2.327 |
3D View
Fluctuation Plot