2-[3-methyl-4-(n-methyl-guanidino)-butyrylamino]-3-(4-phenylethynyl-phenyl)-propionic acid methyl ester (FRG) 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 | 64 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 3151 |
| 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 | 0.83 | 0.83 | 0.84 | 0.83 | 0.83 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 |
| # Exchanges | 4215 | 4124 | 4214 | 4186 | 4132 | 4243 | 4194 | 4233 | 4230 | 4231 | 4274 | 4260 | 4299 | 4297 | 4319 |
| Avg. # Exchanges | 0.84 | 0.82 | 0.84 | 0.84 | 0.83 | 0.85 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.5617 | 0.9279 |
| RMSd_exp | 3.0327 | 0.5920 |
| RMSdist_first | 1.6928 | 0.9319 |
| RMSdist_exp | 2.4604 | 0.7873 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.0771 | 0.6142 |
| RgyrX | 4.5074 | 0.4035 |
| RgyrY | 4.6596 | 0.3822 |
| RgyrZ | 3.0303 | 0.8875 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.9891 |
| Standard deviation (Å) | 0.8030 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| N | 3.929 |
| C | 3.304 |
| N1 | 3.927 |
| N2 | 2.569 |
| C1 | 1.968 |
| C2 | 2.908 |
| C3 | 2.822 |
| C4 | 2.239 |
| C5 | 1.309 |
| C6 | 1.182 |
| C7 | 0.943 |
| O | 1.448 |
| N3 | 0.819 |
| C8 | 1.17 |
| C9 | 1.577 |
| O1 | 1.97 |
| O2 | 2.104 |
| C10 | 2.777 |
| C11 | 1.553 |
| C12 | 1.22 |
| C13 | 1.617 |
| C14 | 1.554 |
| C15 | 1.625 |
| C16 | 1.537 |
| C17 | 1.007 |
| C18 | 1.163 |
| C19 | 1.386 |
| C20 | 1.728 |
| C21 | 2.266 |
| C22 | 2.619 |
| C23 | 2.26 |
| C24 | 2.607 |
| C25 | 2.532 |
3D View
Fluctuation Plot