4-(4-fluorophenyl)-1-(4-piperidinyl)-5-(2-amino-4-pyrimidinyl)-imidazole (SB4) 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 | 45 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 1821 |
| 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 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 |
| # Exchanges | 4178 | 4191 | 4186 | 4183 | 4168 | 4183 | 4241 | 4225 | 4269 | 4241 | 4264 | 4293 | 4278 | 4326 | 4345 |
| Avg. # Exchanges | 0.84 | 0.84 | 0.84 | 0.84 | 0.83 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.87 | 0.87 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 0.8359 | 0.3656 |
| RMSd_exp | 1.1674 | 0.2815 |
| RMSdist_first | 0.3617 | 0.1160 |
| RMSdist_exp | 0.6913 | 0.1260 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 3.7140 | 0.0710 |
| RgyrX | 3.4293 | 0.0814 |
| RgyrY | 2.8553 | 0.0995 |
| RgyrZ | 2.7686 | 0.0615 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 0.5772 |
| Standard deviation (Å) | 0.3614 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| CA1 | 1.342 |
| CA2 | 1.307 |
| NA3 | 0.791 |
| CA4 | 1.243 |
| CA5 | 1.269 |
| CA6 | 0.326 |
| CB1 | 0.721 |
| CB2 | 0.744 |
| CB3 | 0.276 |
| CB4 | 0.714 |
| CB5 | 0.703 |
| CB6 | 0.152 |
| FB7 | 0.445 |
| CC1 | 0.441 |
| CC2 | 0.244 |
| NC3 | 0.386 |
| CC4 | 0.416 |
| NC5 | 0.397 |
| CC6 | 0.493 |
| NC7 | 0.7 |
| ND1 | 0.257 |
| CD2 | 0.314 |
| ND3 | 0.298 |
| CD4 | 0.215 |
| CD5 | 0.235 |
3D View
Fluctuation Plot