N-(p-cyanophenyl)-n'-diphenylmethyl-guanidine-acetic acid (GAS) 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 | 49 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1900 |
| 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 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.86 | 0.86 |
| # Exchanges | 4164 | 4273 | 4232 | 4211 | 4245 | 4232 | 4281 | 4262 | 4260 | 4298 | 4307 | 4283 | 4303 | 4322 | 4348 |
| Avg. # Exchanges | 0.83 | 0.85 | 0.85 | 0.84 | 0.85 | 0.85 | 0.86 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.9918 | 0.6132 |
| RMSd_exp | 2.8407 | 0.5896 |
| RMSdist_first | 1.3350 | 0.3094 |
| RMSdist_exp | 1.2946 | 0.2783 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.0538 | 0.1345 |
| RgyrX | 3.5502 | 0.1389 |
| RgyrY | 3.2759 | 0.1498 |
| RgyrZ | 3.0760 | 0.2543 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.8752 |
| Standard deviation (Å) | 0.8400 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C | 1.957 |
| C1 | 2.775 |
| C2 | 2.984 |
| C3 | 2.747 |
| C4 | 1.923 |
| C5 | 1.076 |
| C6 | 0.716 |
| N | 0.858 |
| C7 | 1.468 |
| C8 | 2.357 |
| C9 | 3.454 |
| C10 | 3.872 |
| C11 | 3.49 |
| C12 | 2.402 |
| C13 | 0.938 |
| N1 | 1.296 |
| C14 | 1.582 |
| C15 | 1.739 |
| O | 2.319 |
| O1 | 2.264 |
| N2 | 1.3 |
| C16 | 0.862 |
| C17 | 1.456 |
| C18 | 1.487 |
| C19 | 0.976 |
| C20 | 1.467 |
| N3 | 1.913 |
| C21 | 1.373 |
| C22 | 1.331 |
3D View
Fluctuation Plot