Pteroic acid (PT1) 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 | 34 |
| Molecule charge (simulated) | -1 |
| System number of atoms | 1282 |
| 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 | 0.80 | 0.81 | 0.81 | 0.81 | 0.82 | 0.81 | 0.82 | 0.82 | 0.83 | 0.82 | 0.83 | 0.83 | 0.83 | 0.84 |
| # Exchanges | 4057 | 4041 | 4009 | 3978 | 4068 | 4122 | 4087 | 4076 | 4138 | 4134 | 4114 | 4177 | 4154 | 4227 | 4166 |
| Avg. # Exchanges | 0.81 | 0.81 | 0.80 | 0.80 | 0.81 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.82 | 0.84 | 0.83 | 0.85 | 0.83 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.5404 | 0.3612 |
| RMSd_exp | 2.2623 | 0.4635 |
| RMSdist_first | 0.6842 | 0.2126 |
| RMSdist_exp | 1.5780 | 0.4346 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.5034 | 0.2861 |
| RgyrX | 3.9036 | 0.2684 |
| RgyrY | 2.7581 | 0.0771 |
| RgyrZ | 4.2063 | 0.3300 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.2187 |
| Standard deviation (Å) | 0.3635 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C2 | 0.975 |
| C3 | 0.426 |
| C5 | 0.717 |
| N6 | 0.894 |
| C7 | 1.031 |
| N9 | 1.025 |
| C10 | 1.195 |
| N11 | 1.578 |
| C12 | 1.494 |
| C21 | 1.154 |
| O22 | 1.728 |
| O1 | 1.667 |
| N4 | 1.096 |
| N8 | 1.393 |
| C13 | 1.766 |
| N14 | 1.43 |
| C15 | 0.875 |
| C16 | 1.38 |
| C17 | 1.302 |
| C18 | 1.285 |
| C19 | 1.242 |
| C20 | 0.596 |
| O23 | 1.782 |
3D View
Fluctuation Plot