Folic acid (FOL) 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 | 49 |
| Molecule charge (simulated) | -2 |
| System number of atoms | 2902 |
| 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 | 0.73 | 0.74 | 0.73 | 0.74 | 0.74 | 0.76 | 0.75 | 0.75 | 0.76 | 0.76 | 0.76 | 0.77 | 0.77 | 0.78 | 0.78 |
| # Exchanges | 3697 | 3667 | 3703 | 3690 | 3772 | 3740 | 3721 | 3757 | 3817 | 3782 | 3823 | 3819 | 3844 | 3880 | 3947 |
| Avg. # Exchanges | 0.74 | 0.73 | 0.74 | 0.74 | 0.75 | 0.75 | 0.74 | 0.75 | 0.76 | 0.76 | 0.76 | 0.76 | 0.77 | 0.78 | 0.79 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.9712 | 0.5071 |
| RMSd_exp | 2.0438 | 0.4537 |
| RMSdist_first | 1.0405 | 0.4649 |
| RMSdist_exp | 1.0875 | 0.3492 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.8273 | 0.4359 |
| RgyrX | 5.0954 | 0.3836 |
| RgyrY | 5.4551 | 0.5002 |
| RgyrZ | 3.4860 | 0.1569 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.6227 |
| Standard deviation (Å) | 0.5437 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| N1 | 1.858 |
| C2 | 1.751 |
| NA2 | 2.48 |
| N3 | 1.738 |
| C4 | 1.604 |
| O4 | 2.636 |
| C4A | 0.688 |
| N5 | 1.038 |
| C6 | 1.172 |
| C7 | 1.902 |
| N8 | 2.113 |
| C8A | 1.266 |
| C9 | 1.826 |
| N10 | 1.699 |
| C11 | 0.808 |
| C12 | 1.514 |
| C13 | 1.684 |
| C14 | 1.306 |
| C15 | 1.617 |
| C16 | 1.457 |
| C | 0.911 |
| O | 1.693 |
| N | 0.685 |
| CA | 0.943 |
| CB | 0.955 |
| CG | 1.353 |
| CD | 1.872 |
| OE1 | 2.46 |
| OE2 | 2.414 |
| CT | 1.741 |
| O1 | 2.401 |
| O2 | 2.34 |
3D View
Fluctuation Plot