3-(4-methoxyphenyl)-5-({[4-(4-methoxyphenyl)-5-methyl-4h-1,2,4-triazol-3-yl]sulfanyl}methyl)-1,2,4-oxadiazole (34M) 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 | 48 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 2616 |
| 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 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 |
| # Exchanges | 4234 | 4256 | 4230 | 4243 | 4261 | 4277 | 4285 | 4281 | 4309 | 4313 | 4356 | 4348 | 4346 | 4350 | 4374 |
| Avg. # Exchanges | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.3761 | 0.6895 |
| RMSd_exp | 2.0794 | 0.5339 |
| RMSdist_first | 1.3867 | 0.4062 |
| RMSdist_exp | 1.4180 | 0.5639 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.6549 | 0.4741 |
| RgyrX | 2.9799 | 0.2550 |
| RgyrY | 4.4351 | 0.5009 |
| RgyrZ | 3.7973 | 0.7073 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.7270 |
| Standard deviation (Å) | 0.5975 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| S1 | 1.96 |
| C2 | 2.493 |
| C5 | 1.863 |
| N6 | 1.468 |
| C7 | 1.111 |
| N8 | 2.046 |
| O9 | 2.327 |
| C10 | 0.767 |
| C11 | 1.462 |
| C13 | 1.779 |
| C15 | 1.646 |
| C16 | 1.799 |
| C18 | 1.471 |
| O20 | 2.331 |
| C21 | 2.91 |
| C25 | 0.822 |
| N26 | 0.764 |
| C27 | 1.664 |
| N28 | 1.669 |
| N29 | 1.136 |
| C30 | 2.8 |
| C34 | 0.756 |
| C35 | 1.377 |
| C37 | 1.757 |
| C39 | 1.694 |
| C40 | 1.73 |
| C42 | 1.379 |
| O44 | 2.275 |
| C45 | 2.826 |
3D View
Fluctuation Plot