1-[n-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-d-phenylalanyl]piperidine (MID) 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 | 69 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 2088 |
| 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 | 0.77 | 0.77 | 0.78 | 0.79 | 0.79 | 0.80 | 0.80 | 0.80 | 0.81 | 0.81 | 0.82 | 0.81 | 0.82 | 0.83 | 0.83 |
| # Exchanges | 3854 | 3878 | 3938 | 3931 | 3949 | 3988 | 4001 | 4066 | 4049 | 4087 | 4083 | 4064 | 4092 | 4144 | 4133 |
| Avg. # Exchanges | 0.77 | 0.78 | 0.79 | 0.79 | 0.79 | 0.80 | 0.80 | 0.81 | 0.81 | 0.82 | 0.82 | 0.81 | 0.82 | 0.83 | 0.83 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 3.0981 | 0.5426 |
| RMSd_exp | 3.0550 | 0.6780 |
| RMSdist_first | 2.0535 | 0.3961 |
| RMSdist_exp | 1.8674 | 0.5044 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.6213 | 0.4509 |
| RgyrX | 4.2315 | 0.4985 |
| RgyrY | 3.5004 | 0.2879 |
| RgyrZ | 3.5128 | 0.5393 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 2.3599 |
| Standard deviation (Å) | 0.8792 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| S | 1.318 |
| O1S | 2.198 |
| O2S | 2.055 |
| C1 | 1.714 |
| C2 | 1.069 |
| C3 | 2.073 |
| C4 | 2.947 |
| C5 | 4.245 |
| C6 | 4.841 |
| C7 | 4.621 |
| C8 | 3.652 |
| C9 | 2.633 |
| C10 | 3.091 |
| N | 1.908 |
| CA | 2.31 |
| C | 1.885 |
| O | 2.138 |
| N1 | 1.691 |
| CA1 | 1.55 |
| CB | 1.881 |
| O1 | 2.418 |
| CB1 | 1.89 |
| CG | 1.204 |
| CD1 | 1.572 |
| CD2 | 1.601 |
| CE1 | 1.692 |
| CE2 | 1.767 |
| CZ | 1.558 |
| CF | 2.353 |
| NG1 | 2.964 |
| NG2 | 3.063 |
| N11 | 2.043 |
| C21 | 2.23 |
| C31 | 2.632 |
| C41 | 2.929 |
| C51 | 2.91 |
| C61 | 2.67 |
3D View
Fluctuation Plot