Methylamino-phenylalanyl-leucyl-hydroxamic acid (PLH) 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 | 52 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1708 |
| 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 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.85 | 0.86 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 | 0.87 |
| # Exchanges | 4194 | 4216 | 4260 | 4258 | 4264 | 4305 | 4317 | 4286 | 4282 | 4286 | 4334 | 4304 | 4286 | 4319 | 4381 |
| Avg. # Exchanges | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 | 0.86 | 0.86 | 0.86 | 0.88 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.1684 | 0.5941 |
| RMSd_exp | 2.1209 | 0.4832 |
| RMSdist_first | 1.0556 | 0.2644 |
| RMSdist_exp | 1.1656 | 0.1881 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 3.7539 | 0.1541 |
| RgyrX | 3.1115 | 0.1203 |
| RgyrY | 2.9310 | 0.1742 |
| RgyrZ | 3.1357 | 0.2850 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.5390 |
| Standard deviation (Å) | 0.7683 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 1.119 |
| C2 | 0.864 |
| C3 | 0.798 |
| C4 | 1.781 |
| C5 | 2.549 |
| C6 | 3.188 |
| C7 | 3.458 |
| C8 | 0.594 |
| C9 | 0.773 |
| C10 | 0.984 |
| C11 | 1.823 |
| C12 | 1.271 |
| C13 | 0.514 |
| C14 | 1.393 |
| C15 | 1.907 |
| C16 | 1.844 |
| C17 | 1.765 |
| C18 | 1.298 |
| N1 | 1.77 |
| N2 | 0.546 |
| N3 | 1.247 |
| O1 | 2.692 |
| O2 | 1.799 |
| O3 | 1.08 |
| O4 | 1.417 |
3D View
Fluctuation Plot