3-[(3'-aminomethyl-biphenyl-4-carbonyl)-amino]-2-(3-carbamimidoyl-benzyl)-butyric acid methyl ester (RPR) 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 | 66 |
| Molecule charge (simulated) | 2 |
| System number of atoms | 2829 |
| 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 | 0.80 | 0.80 | 0.80 | 0.80 | 0.81 | 0.81 | 0.81 | 0.82 | 0.81 | 0.82 | 0.82 | 0.82 |
| # Exchanges | 3882 | 3981 | 3947 | 3968 | 4032 | 4020 | 3995 | 4055 | 4017 | 4062 | 4088 | 4027 | 4143 | 4113 | 4122 |
| Avg. # Exchanges | 0.78 | 0.80 | 0.79 | 0.79 | 0.81 | 0.80 | 0.80 | 0.81 | 0.80 | 0.81 | 0.82 | 0.81 | 0.83 | 0.82 | 0.82 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.3528 | 0.8285 |
| RMSd_exp | 2.5704 | 0.5343 |
| RMSdist_first | 1.6042 | 0.7844 |
| RMSdist_exp | 1.6651 | 0.5984 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.1755 | 0.4470 |
| RgyrX | 3.2455 | 0.7319 |
| RgyrY | 4.2532 | 0.1544 |
| RgyrZ | 4.9546 | 0.4906 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.8408 |
| Standard deviation (Å) | 0.7794 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C | 1.212 |
| C1 | 1.07 |
| C2 | 2.055 |
| C3 | 2.259 |
| C4 | 1.594 |
| C5 | 1.39 |
| C6 | 1.517 |
| C7 | 0.931 |
| C8 | 1.455 |
| C9 | 1.466 |
| C10 | 0.901 |
| C11 | 1.498 |
| C12 | 1.129 |
| N | 0.971 |
| C13 | 1.105 |
| C14 | 1.819 |
| C15 | 0.789 |
| C16 | 1.518 |
| O | 2.162 |
| C17 | 1.156 |
| C18 | 2.287 |
| N1 | 2.906 |
| C19 | 1.312 |
| C20 | 2.098 |
| C21 | 2.702 |
| C22 | 2.865 |
| C23 | 2.182 |
| C24 | 1.093 |
| C25 | 2.939 |
| N2 | 3.753 |
| N3 | 3.419 |
| O1 | 2.201 |
| O2 | 1.684 |
| C26 | 3.15 |
3D View
Fluctuation Plot