2,4-thiazolidiinedione, 5-[[4-[2-(methyl-2-pyridinylamino)ethoxy]phenyl]methyl]-(9cl) (BRL) 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 | 44 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1961 |
| 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 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 | 0.88 | 0.88 | 0.89 | 0.89 | 0.89 | 0.89 | 0.89 | 0.89 |
| # Exchanges | 4335 | 4372 | 4358 | 4341 | 4371 | 4391 | 4409 | 4407 | 4400 | 4419 | 4390 | 4466 | 4482 | 4461 | 4446 |
| Avg. # Exchanges | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 | 0.88 | 0.88 | 0.88 | 0.88 | 0.88 | 0.89 | 0.90 | 0.89 | 0.89 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.9908 | 0.4359 |
| RMSd_exp | 2.0995 | 0.4090 |
| RMSdist_first | 1.2003 | 0.5893 |
| RMSdist_exp | 1.1448 | 0.4378 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.6653 | 0.4973 |
| RgyrX | 3.5629 | 0.3437 |
| RgyrY | 4.4230 | 0.5981 |
| RgyrZ | 3.3503 | 0.2595 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.7387 |
| Standard deviation (Å) | 0.4948 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| S1 | 1.204 |
| O2 | 2.328 |
| O4 | 1.94 |
| O13 | 1.862 |
| N3 | 1.669 |
| N16 | 1.305 |
| N18 | 1.591 |
| C2 | 1.588 |
| C4 | 1.263 |
| C5 | 0.761 |
| C6 | 1.405 |
| C7 | 1.22 |
| C8 | 1.714 |
| C9 | 1.814 |
| C10 | 1.505 |
| C11 | 1.816 |
| C12 | 1.696 |
| C14 | 1.831 |
| C15 | 1.803 |
| C16 | 2.467 |
| C17 | 0.969 |
| C19 | 2.378 |
| C20 | 2.796 |
| C21 | 2.679 |
| C22 | 1.864 |
3D View
Fluctuation Plot