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 | 3078 |
| 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 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.84 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 |
| # Exchanges | 4050 | 4050 | 4092 | 4083 | 4069 | 4138 | 4132 | 4153 | 4168 | 4176 | 4199 | 4178 | 4209 | 4194 | 4171 |
| Avg. # Exchanges | 0.81 | 0.81 | 0.82 | 0.82 | 0.81 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 | 0.83 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.6363 | 0.8374 |
| RMSd_exp | 2.3728 | 0.5889 |
| RMSdist_first | 1.9023 | 0.8669 |
| RMSdist_exp | 1.5459 | 0.6779 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.9316 | 0.4394 |
| RgyrX | 3.9468 | 0.1479 |
| RgyrY | 5.4368 | 0.4873 |
| RgyrZ | 5.0028 | 0.5743 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.6441 |
| Standard deviation (Å) | 0.7848 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C | 3.151 |
| C1 | 2.256 |
| C2 | 1.489 |
| C3 | 2.377 |
| N | 3.329 |
| C4 | 3.524 |
| C5 | 0.898 |
| C6 | 1.732 |
| C7 | 2.554 |
| N1 | 2.275 |
| C8 | 1.125 |
| N2 | 0.713 |
| N3 | 0.98 |
| C9 | 0.651 |
| C10 | 0.68 |
| C11 | 0.935 |
| C12 | 0.954 |
| C13 | 0.71 |
| C14 | 0.664 |
| N4 | 0.842 |
| C15 | 1.281 |
| C16 | 1.21 |
| C17 | 1.701 |
| C18 | 1.763 |
| C19 | 1.356 |
| C20 | 1.768 |
| C21 | 1.722 |
| C22 | 1.56 |
| N5 | 0.901 |
| C23 | 1.529 |
| C24 | 2.22 |
| N6 | 2.342 |
| C25 | 2.806 |
| C26 | 2.245 |
| C27 | 1.552 |
| O | 2.182 |
| C28 | 0.853 |
3D View
Fluctuation Plot