6-(2,5-dimethoxy-benzyl)-5-methyl-pyrido[2,3-d]pyrimidine-2,4-diamine (MXA) 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 | 43 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1978 |
| 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 | 0.82 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 | 0.87 |
| # Exchanges | 4134 | 4135 | 4196 | 4202 | 4174 | 4211 | 4272 | 4261 | 4269 | 4298 | 4283 | 4283 | 4288 | 4326 | 4376 |
| Avg. # Exchanges | 0.83 | 0.83 | 0.84 | 0.84 | 0.83 | 0.84 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 | 0.88 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.6036 | 0.5477 |
| RMSd_exp | 1.8104 | 0.4758 |
| RMSdist_first | 0.6613 | 0.2751 |
| RMSdist_exp | 0.6746 | 0.2093 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 3.8568 | 0.0993 |
| RgyrX | 3.4684 | 0.1651 |
| RgyrY | 3.5304 | 0.1041 |
| RgyrZ | 2.2843 | 0.1412 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.3265 |
| Standard deviation (Å) | 0.5442 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| N1 | 1.389 |
| C2 | 0.819 |
| N2 | 1.394 |
| N3 | 1.037 |
| C4 | 1.2 |
| N4 | 2.442 |
| C4A | 0.463 |
| C5 | 1.024 |
| C5M | 2.325 |
| C6 | 1.013 |
| C7 | 1.702 |
| N8 | 1.878 |
| C8A | 0.943 |
| C9 | 1.47 |
| C1' | 0.638 |
| C2' | 0.782 |
| O2' | 1.463 |
| C21 | 2.381 |
| C3' | 1.255 |
| C4' | 0.98 |
| C5' | 0.764 |
| O5' | 1.451 |
| C51 | 2.025 |
| C6' | 0.999 |
3D View
Fluctuation Plot