Ethyl [(1r,3ar,4ar,6r,8ar,9s,9as)-9-{(e)-2-[5-(3-fluorophenyl)pyridin-2-yl]ethenyl}-1-methyl-3-oxododecahydronaphtho[2,3-c]furan-6-yl]carbamate (VPX) 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 | 71 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 3749 |
| 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 | 0.86 | 0.85 | 0.86 | 0.86 | 0.86 | 0.87 | 0.87 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 |
| # Exchanges | 4311 | 4237 | 4293 | 4298 | 4289 | 4339 | 4329 | 4322 | 4336 | 4360 | 4356 | 4398 | 4396 | 4376 | 4364 |
| Avg. # Exchanges | 0.86 | 0.85 | 0.86 | 0.86 | 0.86 | 0.87 | 0.87 | 0.86 | 0.87 | 0.87 | 0.87 | 0.88 | 0.88 | 0.88 | 0.87 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.1776 | 0.3866 |
| RMSd_exp | 1.4722 | 0.5111 |
| RMSdist_first | 1.3014 | 0.1789 |
| RMSdist_exp | 0.7184 | 0.3666 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.7941 | 0.3180 |
| RgyrX | 5.1350 | 0.4462 |
| RgyrY | 5.6540 | 0.3750 |
| RgyrZ | 2.9339 | 0.2458 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.1504 |
| Standard deviation (Å) | 0.4725 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| CAA | 1.831 |
| CAO | 1.281 |
| OAV | 0.882 |
| CAX | 0.833 |
| OAC | 1.424 |
| NAU | 0.634 |
| CBE | 0.666 |
| CAR | 0.686 |
| CAP | 0.936 |
| CAQ | 1.051 |
| CBI | 0.588 |
| CBG | 0.62 |
| CAS | 0.818 |
| CBH | 0.752 |
| CAY | 0.986 |
| OAD | 1.493 |
| OAW | 0.86 |
| CBD | 0.618 |
| CAB | 0.991 |
| CBJ | 0.462 |
| CBF | 0.795 |
| CAG | 1.316 |
| CAF | 1.682 |
| CBA | 1.225 |
| CAK | 1.621 |
| CAL | 1.455 |
| NAT | 1.553 |
| CAM | 1.343 |
| CBB | 0.636 |
| CBC | 0.748 |
| CAN | 1.277 |
| CAZ | 1.564 |
| FAE | 2.53 |
| CAI | 1.551 |
| CAH | 1.985 |
| CAJ | 1.723 |
3D View
Fluctuation Plot