O6-cyclohexylmethoxy-2-(4'-sulphamoylanilino) purine (4SP) 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 | 50 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1880 |
| 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 | 0.74 | 0.75 | 0.76 | 0.77 | 0.79 | 0.80 | 0.81 | 0.81 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 |
| # Exchanges | 3659 | 3748 | 3819 | 3855 | 3936 | 4005 | 4030 | 4089 | 4110 | 4159 | 4180 | 4194 | 4200 | 4233 | 4247 |
| Avg. # Exchanges | 0.73 | 0.75 | 0.76 | 0.77 | 0.79 | 0.80 | 0.81 | 0.82 | 0.82 | 0.83 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.7826 | 0.2576 |
| RMSd_exp | 2.1724 | 0.6621 |
| RMSdist_first | 0.9886 | 0.1875 |
| RMSdist_exp | 1.4991 | 0.5078 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.9443 | 0.2917 |
| RgyrX | 3.9281 | 0.3084 |
| RgyrY | 4.2992 | 0.2712 |
| RgyrZ | 3.8678 | 0.1492 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.2486 |
| Standard deviation (Å) | 0.4600 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C2 | 0.971 |
| C8 | 1.087 |
| C10 | 1.211 |
| C11 | 1.112 |
| C12 | 1.735 |
| C13 | 2.086 |
| C14 | 1.93 |
| C15 | 2.019 |
| C16 | 1.683 |
| C19 | 1.289 |
| C20 | 0.48 |
| C21 | 1.255 |
| C22 | 1.371 |
| N26 | 1.816 |
| N1 | 0.913 |
| C6 | 0.617 |
| O6 | 0.875 |
| C5 | 0.5 |
| N7 | 0.706 |
| N9 | 1.145 |
| C4 | 0.794 |
| N3 | 0.982 |
| N2 | 1.424 |
| C17 | 0.897 |
| C18 | 1.382 |
| S23 | 1.027 |
| O24 | 1.868 |
| O25 | 1.786 |
3D View
Fluctuation Plot