N~3~-cyclopropyl-n~4~'-(cyclopropylmethyl)-6-methylbiphenyl-3,4'-dicarboxamide (GK5) 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 | 50 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 3050 |
| 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 | 0.87 | 0.88 | 0.88 | 0.88 | 0.88 | 0.88 | 0.88 | 0.89 | 0.89 | 0.88 | 0.89 | 0.89 | 0.89 | 0.89 | 0.90 |
| # Exchanges | 4374 | 4401 | 4346 | 4367 | 4353 | 4356 | 4434 | 4454 | 4476 | 4447 | 4445 | 4438 | 4461 | 4469 | 4493 |
| Avg. # Exchanges | 0.87 | 0.88 | 0.87 | 0.87 | 0.87 | 0.87 | 0.89 | 0.89 | 0.90 | 0.89 | 0.89 | 0.89 | 0.89 | 0.89 | 0.90 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.6434 | 0.4199 |
| RMSd_exp | 1.3320 | 0.3312 |
| RMSdist_first | 0.9085 | 0.2819 |
| RMSdist_exp | 0.5875 | 0.2004 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.0475 | 0.1462 |
| RgyrX | 4.4907 | 0.2255 |
| RgyrY | 4.5616 | 0.1321 |
| RgyrZ | 3.1540 | 0.0823 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 0.9666 |
| Standard deviation (Å) | 0.5597 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C9 | 0.657 |
| C22 | 1.796 |
| C21 | 1.793 |
| C18 | 0.895 |
| C26 | 2.07 |
| C25 | 2.058 |
| C24 | 1.294 |
| C4 | 0.428 |
| C8 | 0.535 |
| C13 | 0.49 |
| C7 | 0.397 |
| C12 | 0.61 |
| O16 | 1.594 |
| N15 | 0.759 |
| C3 | 0.361 |
| C1 | 0.314 |
| C2 | 0.439 |
| C5 | 0.837 |
| C10 | 0.95 |
| C14 | 0.773 |
| C11 | 0.922 |
| C6 | 0.813 |
| C17 | 1.009 |
| O20 | 2.059 |
| N19 | 0.59 |
| C23 | 0.689 |
3D View
Fluctuation Plot