9-(4-hydroxybutyl)-n2-phenylguanine (BPG) 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 | 39 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1428 |
| 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 | 0.86 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 | 0.88 | 0.88 | 0.88 | 0.88 | 0.89 |
| # Exchanges | 4297 | 4311 | 4325 | 4312 | 4336 | 4354 | 4388 | 4366 | 4364 | 4364 | 4397 | 4415 | 4384 | 4391 | 4420 |
| Avg. # Exchanges | 0.86 | 0.86 | 0.87 | 0.86 | 0.87 | 0.87 | 0.88 | 0.87 | 0.87 | 0.87 | 0.88 | 0.88 | 0.88 | 0.88 | 0.88 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.3115 | 0.3821 |
| RMSd_exp | 1.9807 | 0.3537 |
| RMSdist_first | 0.6590 | 0.3292 |
| RMSdist_exp | 1.4546 | 0.2879 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.0038 | 0.1813 |
| RgyrX | 3.5987 | 0.2883 |
| RgyrY | 2.0110 | 0.2225 |
| RgyrZ | 3.8675 | 0.2071 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 0.9172 |
| Standard deviation (Å) | 0.4074 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C3' | 1.329 |
| O3' | 1.92 |
| C2' | 0.959 |
| C12 | 0.888 |
| C1' | 1.272 |
| N9 | 0.724 |
| C4 | 0.473 |
| N3 | 0.702 |
| C2 | 0.526 |
| N2 | 0.794 |
| N1 | 0.58 |
| C6 | 0.667 |
| O6 | 1.133 |
| C5 | 0.349 |
| N7 | 0.507 |
| C8 | 0.552 |
| C04 | 1.023 |
| C05 | 1.392 |
| C06 | 1.231 |
| C01 | 0.396 |
| C02 | 1.296 |
| C03 | 1.466 |
3D View
Fluctuation Plot