4-(4-methyl-piperazin-1-ylmethyl)-n-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-benzamide (STI) 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 | 69 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 4290 |
| 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 | 0.81 | 0.81 | 0.81 | 0.81 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.85 |
| # Exchanges | 4034 | 4084 | 4046 | 4066 | 4112 | 4106 | 4100 | 4140 | 4176 | 4130 | 4188 | 4183 | 4235 | 4205 | 4207 |
| Avg. # Exchanges | 0.81 | 0.82 | 0.81 | 0.81 | 0.82 | 0.82 | 0.82 | 0.83 | 0.84 | 0.83 | 0.84 | 0.84 | 0.85 | 0.84 | 0.84 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.2625 | 0.5111 |
| RMSd_exp | 2.6857 | 0.7018 |
| RMSdist_first | 1.3230 | 0.4397 |
| RMSdist_exp | 1.8761 | 0.8722 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.9766 | 0.4485 |
| RgyrX | 5.3696 | 0.6490 |
| RgyrY | 5.1322 | 0.3960 |
| RgyrZ | 4.0098 | 0.1154 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.6951 |
| Standard deviation (Å) | 0.7331 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C | 2.908 |
| C1 | 2.049 |
| C2 | 1.458 |
| C3 | 2.408 |
| N | 3.398 |
| C4 | 3.473 |
| C5 | 0.943 |
| C6 | 1.835 |
| C7 | 2.637 |
| N1 | 2.348 |
| C8 | 1.224 |
| N2 | 0.752 |
| N3 | 1.181 |
| C9 | 0.9 |
| C10 | 1.142 |
| C11 | 1.344 |
| C12 | 1.156 |
| C13 | 0.746 |
| C14 | 0.747 |
| N4 | 0.754 |
| C15 | 1.104 |
| C16 | 1.084 |
| C17 | 1.672 |
| C18 | 1.782 |
| C19 | 1.404 |
| C20 | 1.754 |
| C21 | 1.632 |
| C22 | 1.698 |
| N5 | 0.963 |
| C23 | 1.594 |
| C24 | 2.086 |
| N6 | 2.134 |
| C25 | 3.208 |
| C26 | 2.094 |
| C27 | 1.56 |
| O | 2.056 |
| C28 | 1.491 |
3D View
Fluctuation Plot