[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 | 2087 |
| 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 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 |
| # Exchanges | 4167 | 4185 | 4248 | 4173 | 4214 | 4206 | 4239 | 4250 | 4276 | 4245 | 4238 | 4217 | 4293 | 4263 | 4306 |
| Avg. # Exchanges | 0.83 | 0.84 | 0.85 | 0.83 | 0.84 | 0.84 | 0.85 | 0.85 | 0.86 | 0.85 | 0.85 | 0.84 | 0.86 | 0.85 | 0.86 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.7849 | 0.5730 |
| RMSd_exp | 2.4744 | 0.5732 |
| RMSdist_first | 0.8364 | 0.2382 |
| RMSdist_exp | 1.5801 | 0.3708 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.6738 | 0.2205 |
| RgyrX | 5.1240 | 0.2389 |
| RgyrY | 4.6818 | 0.2427 |
| RgyrZ | 4.0226 | 0.0951 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.3887 |
| Standard deviation (Å) | 0.4047 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| N | 1.506 |
| C | 1.752 |
| C1 | 1.527 |
| C2 | 1.497 |
| C3 | 1.736 |
| C4 | 0.817 |
| N1 | 0.823 |
| C5 | 1.528 |
| C6 | 1.531 |
| C7 | 1.53 |
| C8 | 1.579 |
| C9 | 1.007 |
| C10 | 1.404 |
| O | 2.392 |
| N2 | 1.23 |
| C11 | 1.249 |
| C12 | 1.11 |
| C13 | 1.658 |
| C14 | 2.052 |
| N3 | 0.701 |
| S | 1.03 |
| O1 | 1.645 |
| O2 | 1.623 |
| C15 | 0.672 |
| C16 | 0.829 |
| C17 | 1.571 |
| C18 | 1.716 |
| C19 | 0.759 |
| C20 | 0.912 |
| C21 | 1.288 |
| C22 | 1.768 |
| C23 | 1.703 |
| C24 | 1.28 |
| CL | 1.792 |
3D View
Fluctuation Plot