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 | 1777 |
| 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 | 0.72 | 0.73 | 0.74 | 0.74 | 0.74 | 0.75 | 0.75 | 0.75 | 0.75 | 0.76 | 0.77 | 0.76 | 0.77 | 0.78 | 0.78 |
| # Exchanges | 3624 | 3646 | 3676 | 3695 | 3707 | 3757 | 3744 | 3779 | 3784 | 3741 | 3815 | 3795 | 3817 | 3844 | 3890 |
| Avg. # Exchanges | 0.72 | 0.73 | 0.74 | 0.74 | 0.74 | 0.75 | 0.75 | 0.76 | 0.76 | 0.75 | 0.76 | 0.76 | 0.76 | 0.77 | 0.78 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.5900 | 0.4173 |
| RMSd_exp | 2.8341 | 0.4508 |
| RMSdist_first | 1.6408 | 0.3083 |
| RMSdist_exp | 2.0916 | 0.4260 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.9393 | 0.3637 |
| RgyrX | 2.6737 | 0.1453 |
| RgyrY | 5.7450 | 0.4542 |
| RgyrZ | 5.5048 | 0.3609 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.5197 |
| Standard deviation (Å) | 0.5068 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| N1 | 1.725 |
| C2 | 1.675 |
| NA2 | 2.383 |
| N3 | 1.774 |
| C4 | 1.587 |
| O4 | 2.623 |
| C4A | 0.584 |
| N5 | 0.952 |
| C6 | 1.305 |
| C7 | 2.07 |
| N8 | 2.148 |
| C8A | 1.203 |
| C9 | 1.965 |
| N10 | 1.73 |
| C11 | 0.937 |
| C12 | 1.603 |
| C13 | 1.773 |
| C14 | 1.427 |
| C15 | 1.742 |
| C16 | 1.571 |
| C | 0.832 |
| O | 1.344 |
| N | 0.6 |
| CA | 0.701 |
| CB | 0.933 |
| CG | 1.268 |
| CD | 1.581 |
| OE1 | 2.093 |
| OE2 | 2.123 |
| CT | 1.068 |
| O1 | 1.67 |
| O2 | 1.639 |
3D View
Fluctuation Plot