(4r)-2-(2-ethoxyethyl)-4-(ethylamino)-3,4-dihydro-2h-thieno[3,2-e][1,2]thiazine-6-sulfonamide 1,1-dioxide (BZU) 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 | 44 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1706 |
| 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 | 0.72 | 0.74 | 0.76 | 0.78 | 0.79 | 0.80 | 0.81 | 0.82 | 0.83 | 0.83 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 |
| # Exchanges | 3657 | 3718 | 3764 | 3892 | 3967 | 4015 | 4074 | 4125 | 4124 | 4171 | 4237 | 4244 | 4272 | 4236 | 4296 |
| Avg. # Exchanges | 0.73 | 0.74 | 0.75 | 0.78 | 0.79 | 0.80 | 0.81 | 0.83 | 0.82 | 0.83 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.6303 | 0.2994 |
| RMSd_exp | 2.0294 | 0.3395 |
| RMSdist_first | 0.7046 | 0.1668 |
| RMSdist_exp | 0.9005 | 0.1101 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 3.8256 | 0.1092 |
| RgyrX | 2.2919 | 0.1044 |
| RgyrY | 3.2990 | 0.1392 |
| RgyrZ | 3.6210 | 0.1234 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 0.8466 |
| Standard deviation (Å) | 0.5361 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| N | 0.591 |
| C | 0.695 |
| C1 | 0.441 |
| C2 | 0.287 |
| C3 | 0.343 |
| S | 0.562 |
| S1 | 0.352 |
| C4 | 0.217 |
| C5 | 0.252 |
| S2 | 0.443 |
| N1 | 1.501 |
| N2 | 0.644 |
| C6 | 1.04 |
| C7 | 1.199 |
| O | 0.789 |
| O1 | 0.685 |
| C8 | 0.889 |
| C9 | 0.729 |
| O2 | 0.901 |
| C10 | 1.528 |
| C11 | 2.484 |
| O3 | 1.456 |
| O4 | 1.443 |
3D View
Fluctuation Plot