N-({1-[(2s)-2-carboxy-4-phenylbutyl]cyclopentyl}carbonyl)-l-tryptophan (0DB) 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 | 65 |
| Molecule charge (simulated) | -2 |
| System number of atoms | 1973 |
| 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 | 0.77 | 0.77 | 0.77 | 0.77 | 0.78 | 0.78 | 0.78 | 0.78 | 0.78 | 0.78 | 0.79 | 0.79 | 0.79 | 0.80 | 0.80 |
| # Exchanges | 3787 | 3848 | 3866 | 3867 | 3833 | 3945 | 3839 | 3928 | 3896 | 3890 | 3952 | 3961 | 3983 | 3947 | 3981 |
| Avg. # Exchanges | 0.76 | 0.77 | 0.77 | 0.77 | 0.77 | 0.79 | 0.77 | 0.79 | 0.78 | 0.78 | 0.79 | 0.79 | 0.80 | 0.79 | 0.80 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.4469 | 0.7047 |
| RMSd_exp | 2.3356 | 0.4426 |
| RMSdist_first | 1.3902 | 0.4144 |
| RMSdist_exp | 1.3007 | 0.2714 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.5355 | 0.2982 |
| RgyrX | 3.7412 | 0.4434 |
| RgyrY | 3.1552 | 0.2752 |
| RgyrZ | 4.1187 | 0.3632 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.8067 |
| Standard deviation (Å) | 0.6796 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| CA | 0.849 |
| CB1 | 0.952 |
| CG | 1.122 |
| CD | 1.134 |
| CE1 | 1.889 |
| CE2 | 1.849 |
| CZ1 | 2.546 |
| CZ2 | 2.507 |
| CH | 2.66 |
| CB2 | 1.644 |
| OG1 | 2.203 |
| OG2 | 2.245 |
| CH2 | 0.871 |
| CA1 | 0.839 |
| 1CB1 | 1 |
| 1CB2 | 1.467 |
| CG1 | 1.535 |
| CG2 | 1.776 |
| C | 1.039 |
| O | 1.946 |
| N | 1.06 |
| CA2 | 1.404 |
| C1 | 2.421 |
| O1 | 3.098 |
| CB | 1.584 |
| CG3 | 1.178 |
| CD1 | 2.128 |
| CD2 | 1.154 |
| NE1 | 2.285 |
| 1CE2 | 1.678 |
| CE3 | 2.021 |
| 1CZ2 | 2.342 |
| CZ3 | 2.863 |
| 1CH2 | 2.838 |
| OXT | 3.106 |
3D View
Fluctuation Plot