[4-(4-acetylamino-phenyl)-3,5-dioxo-4-aza-tricyclo[5.2.2.0 2,6]undec-1-ylcarbamoyloxy]-acetic acid (FRA) 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 | 53 |
| Molecule charge (simulated) | -1 |
| System number of atoms | 2441 |
| 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 | 0.81 | 0.81 | 0.81 | 0.81 | 0.81 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 |
| # Exchanges | 4071 | 4027 | 4051 | 4016 | 4066 | 4148 | 4075 | 4142 | 4145 | 4146 | 4155 | 4172 | 4192 | 4180 | 4177 |
| Avg. # Exchanges | 0.81 | 0.81 | 0.81 | 0.80 | 0.81 | 0.83 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.2805 | 0.2342 |
| RMSd_exp | 1.3070 | 0.1486 |
| RMSdist_first | 0.6414 | 0.1654 |
| RMSdist_exp | 0.6412 | 0.1433 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.6174 | 0.1333 |
| RgyrX | 4.4201 | 0.1243 |
| RgyrY | 2.5742 | 0.0973 |
| RgyrZ | 4.0555 | 0.1995 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 0.7005 |
| Standard deviation (Å) | 0.4297 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C22 | 1.993 |
| C1 | 0.723 |
| O3 | 0.717 |
| N1 | 0.626 |
| C2 | 0.488 |
| C7 | 0.698 |
| C6 | 0.664 |
| C5 | 0.352 |
| C4 | 0.616 |
| C3 | 0.674 |
| N5 | 0.317 |
| C11 | 0.333 |
| C10 | 0.303 |
| C9 | 0.378 |
| C8 | 0.426 |
| O11 | 0.532 |
| O8 | 0.653 |
| C12 | 0.347 |
| C17 | 0.451 |
| C16 | 0.496 |
| C14 | 0.478 |
| C13 | 0.416 |
| C15 | 0.452 |
| N15 | 0.759 |
| C18 | 0.49 |
| O18 | 1.13 |
| O19 | 0.861 |
| C19 | 0.744 |
| C20 | 0.98 |
| O20 | 1.781 |
| O21 | 1.838 |
3D View
Fluctuation Plot