[4-(6-chloro-naphthalene-2-sulfonyl)-piperazin-1-yl]- (3,4,5,6-tetrahydro-2h-[1,4']bipyridinyl-4-yl)- methanone (ZEN) 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 | 62 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 2126 |
| 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 | 0.84 | 0.84 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.85 | 0.86 |
| # Exchanges | 4180 | 4164 | 4188 | 4234 | 4235 | 4207 | 4214 | 4268 | 4253 | 4248 | 4280 | 4288 | 4271 | 4291 | 4293 |
| Avg. # Exchanges | 0.84 | 0.83 | 0.84 | 0.85 | 0.85 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.85 | 0.86 | 0.86 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.7628 | 0.5569 |
| RMSd_exp | 2.3283 | 0.5382 |
| RMSdist_first | 0.7992 | 0.3559 |
| RMSdist_exp | 1.5226 | 0.3783 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.6911 | 0.2169 |
| RgyrX | 5.0690 | 0.3370 |
| RgyrY | 4.4089 | 0.1171 |
| RgyrZ | 4.4269 | 0.1191 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.3558 |
| Standard deviation (Å) | 0.4298 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| N1 | 1.532 |
| C2 | 1.765 |
| C3 | 1.546 |
| C5 | 1.516 |
| C6 | 1.765 |
| C4 | 0.85 |
| N7 | 0.847 |
| C8 | 1.574 |
| C9 | 1.477 |
| C11 | 1.458 |
| C12 | 1.575 |
| C10 | 0.902 |
| C13 | 1.472 |
| O23 | 2.509 |
| N14 | 1.275 |
| C15 | 1.142 |
| C16 | 0.998 |
| C18 | 1.718 |
| C19 | 2.148 |
| N17 | 0.656 |
| S20 | 0.82 |
| O21 | 1.353 |
| O22 | 1.395 |
| C24 | 0.548 |
| C25 | 0.82 |
| C33 | 1.489 |
| C34 | 1.686 |
| C26 | 0.763 |
| C27 | 0.923 |
| C28 | 1.294 |
| C30 | 1.692 |
| C31 | 1.664 |
| C29 | 1.227 |
| CL2 | 1.697 |
3D View
Fluctuation Plot