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 | 1909 |
| 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 | 0.74 | 0.75 | 0.75 | 0.75 | 0.75 | 0.76 | 0.76 | 0.76 | 0.77 | 0.78 | 0.77 | 0.78 | 0.78 | 0.78 |
| # Exchanges | 3709 | 3741 | 3724 | 3753 | 3732 | 3757 | 3793 | 3819 | 3812 | 3865 | 3891 | 3786 | 3898 | 3891 | 3887 |
| Avg. # Exchanges | 0.74 | 0.75 | 0.74 | 0.75 | 0.75 | 0.75 | 0.76 | 0.76 | 0.76 | 0.77 | 0.78 | 0.76 | 0.78 | 0.78 | 0.78 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.7991 | 0.4968 |
| RMSd_exp | 2.7343 | 0.3918 |
| RMSdist_first | 0.8032 | 0.4057 |
| RMSdist_exp | 2.0351 | 0.4177 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.9489 | 0.3500 |
| RgyrX | 2.8565 | 0.0806 |
| RgyrY | 5.6670 | 0.3733 |
| RgyrZ | 5.5181 | 0.3932 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.4993 |
| Standard deviation (Å) | 0.5156 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| N1 | 1.68 |
| C2 | 1.529 |
| NA2 | 2.208 |
| N3 | 1.717 |
| C4 | 1.6 |
| O4 | 2.645 |
| C4A | 0.578 |
| N5 | 0.956 |
| C6 | 1.284 |
| C7 | 2.041 |
| N8 | 2.105 |
| C8A | 1.153 |
| C9 | 1.917 |
| N10 | 1.658 |
| C11 | 0.856 |
| C12 | 1.522 |
| C13 | 1.676 |
| C14 | 1.34 |
| C15 | 1.709 |
| C16 | 1.537 |
| C | 0.801 |
| O | 1.369 |
| N | 0.589 |
| CA | 0.67 |
| CB | 0.91 |
| CG | 1.354 |
| CD | 1.746 |
| OE1 | 2.252 |
| OE2 | 2.299 |
| CT | 1.023 |
| O1 | 1.63 |
| O2 | 1.623 |
3D View
Fluctuation Plot