[((1r)-2-{(2s)-2-[({4-[amino(imino)methyl]benzyl}amino)carbonyl]azetidinyl}-1-cyclohexyl-2-oxoethyl)amino]acetic acid (MEL) 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 | 63 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 1818 |
| 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 | 0.78 | 0.79 | 0.79 | 0.79 | 0.80 | 0.80 | 0.79 | 0.80 | 0.80 | 0.81 | 0.82 | 0.81 | 0.81 | 0.82 | 0.82 |
| # Exchanges | 3939 | 3904 | 3962 | 3946 | 4012 | 4046 | 3989 | 4077 | 4005 | 3994 | 4105 | 4044 | 4102 | 4065 | 4072 |
| Avg. # Exchanges | 0.79 | 0.78 | 0.79 | 0.79 | 0.80 | 0.81 | 0.80 | 0.82 | 0.80 | 0.80 | 0.82 | 0.81 | 0.82 | 0.81 | 0.81 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.1200 | 0.5782 |
| RMSd_exp | 3.2724 | 0.4591 |
| RMSdist_first | 1.2862 | 0.4117 |
| RMSdist_exp | 1.7028 | 0.3676 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.2424 | 0.3849 |
| RgyrX | 3.7038 | 0.5711 |
| RgyrY | 2.7413 | 0.3375 |
| RgyrZ | 3.7894 | 0.5088 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.8165 |
| Standard deviation (Å) | 0.9215 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C | 1.112 |
| C1 | 1.797 |
| C2 | 2.714 |
| C3 | 2.864 |
| C4 | 2.68 |
| C5 | 1.854 |
| N | 1.606 |
| C6 | 0.845 |
| C7 | 0.641 |
| O | 0.934 |
| N1 | 0.85 |
| C8 | 0.982 |
| C9 | 0.894 |
| O1 | 1.029 |
| N2 | 1.169 |
| C10 | 1.626 |
| C11 | 1.111 |
| C12 | 1.522 |
| C13 | 1.633 |
| C14 | 1.291 |
| C15 | 1.598 |
| C16 | 1.574 |
| C17 | 1.87 |
| N3 | 2.55 |
| N4 | 2.414 |
| C18 | 1.37 |
| C19 | 1.382 |
| C20 | 2.627 |
| C21 | 3.556 |
| O2 | 4.113 |
| O3 | 4.103 |
3D View
Fluctuation Plot