4-acetyl-4-guanidino-6-methyl(propyl)carboxamide-4,5-dihydro-2h-pyran-2-carboxylic acid (G20) 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 | 47 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1406 |
| 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 | 0.81 | 0.81 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.83 | 0.84 | 0.84 | 0.85 | 0.85 |
| # Exchanges | 4001 | 4103 | 4061 | 4074 | 4104 | 4136 | 4164 | 4153 | 4153 | 4140 | 4172 | 4169 | 4278 | 4254 | 4196 |
| Avg. # Exchanges | 0.80 | 0.82 | 0.81 | 0.81 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.86 | 0.85 | 0.84 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.5120 | 0.7752 |
| RMSd_exp | 1.3186 | 0.6307 |
| RMSdist_first | 0.7120 | 0.2779 |
| RMSdist_exp | 0.7988 | 0.2676 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 3.6234 | 0.1075 |
| RgyrX | 2.7305 | 0.1127 |
| RgyrY | 3.2686 | 0.2623 |
| RgyrZ | 2.8337 | 0.1759 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.0838 |
| Standard deviation (Å) | 0.6262 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C | 0.538 |
| O | 0.826 |
| O1 | 0.692 |
| C1 | 0.367 |
| C2 | 0.455 |
| C3 | 0.448 |
| C4 | 0.499 |
| N | 1.06 |
| C5 | 1.679 |
| O2 | 1.958 |
| C6 | 2.336 |
| C7 | 0.447 |
| O3 | 0.662 |
| C8 | 0.468 |
| O4 | 0.936 |
| N1 | 0.583 |
| C9 | 1.12 |
| C10 | 0.823 |
| C11 | 1.376 |
| C12 | 2.023 |
| N2 | 1.02 |
| C13 | 1.466 |
| N3 | 2.1 |
| N4 | 2.13 |
3D View
Fluctuation Plot