D-leucyl-n-(4-fluorobenzyl)-l-phenylalaninamide (0FG) 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 | 57 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 2130 |
| 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 | 0.82 | 0.82 | 0.83 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.83 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 |
| # Exchanges | 4105 | 4129 | 4123 | 4173 | 4121 | 4099 | 4093 | 4129 | 4184 | 4139 | 4256 | 4252 | 4234 | 4286 | 4237 |
| Avg. # Exchanges | 0.82 | 0.83 | 0.82 | 0.83 | 0.82 | 0.82 | 0.82 | 0.83 | 0.84 | 0.83 | 0.85 | 0.85 | 0.85 | 0.86 | 0.85 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.7922 | 0.5480 |
| RMSd_exp | 2.3008 | 0.3359 |
| RMSdist_first | 1.1370 | 0.5158 |
| RMSdist_exp | 1.2945 | 0.3112 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.2423 | 0.1893 |
| RgyrX | 3.8137 | 0.2611 |
| RgyrY | 3.5279 | 0.1959 |
| RgyrZ | 2.9790 | 0.3067 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.4705 |
| Standard deviation (Å) | 0.5404 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| N | 1.608 |
| CA | 0.906 |
| CB | 0.989 |
| CG | 1.347 |
| CD1 | 2.162 |
| CD2 | 1.932 |
| C | 0.82 |
| O | 1.132 |
| N1 | 0.814 |
| CA1 | 0.864 |
| C1 | 1.088 |
| O1 | 1.493 |
| CB1 | 1.004 |
| CG1 | 0.788 |
| 1CD1 | 1.674 |
| 1CD2 | 1.692 |
| CE1 | 2.463 |
| CE2 | 2.478 |
| CZ | 2.679 |
| C11 | 0.829 |
| C2 | 1.43 |
| C3 | 1.683 |
| C4 | 1.499 |
| C5 | 1.684 |
| C6 | 1.437 |
| C7 | 1.397 |
| N2 | 1.087 |
| F | 2.195 |
3D View
Fluctuation Plot