1-(5-isoquinolinesulfonyl)-2-methylpiperazine (IQP) 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 | 38 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 1403 |
| 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 | 0.85 | 0.85 | 0.85 | 0.86 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 |
| # Exchanges | 4297 | 4261 | 4259 | 4297 | 4276 | 4307 | 4347 | 4314 | 4304 | 4367 | 4374 | 4316 | 4331 | 4344 | 4409 |
| Avg. # Exchanges | 0.86 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 | 0.87 | 0.86 | 0.86 | 0.87 | 0.87 | 0.86 | 0.87 | 0.87 | 0.88 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.1949 | 0.7286 |
| RMSd_exp | 1.5716 | 0.3948 |
| RMSdist_first | 0.5219 | 0.2571 |
| RMSdist_exp | 0.7319 | 0.1591 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 3.0587 | 0.0550 |
| RgyrX | 2.5159 | 0.0735 |
| RgyrY | 2.4061 | 0.0493 |
| RgyrZ | 2.5657 | 0.0875 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.0932 |
| Standard deviation (Å) | 0.4843 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.304 |
| C2 | 1.002 |
| C3 | 1.518 |
| C4 | 1.297 |
| C5 | 0.559 |
| C6 | 0.675 |
| N7 | 0.922 |
| C8 | 1.224 |
| C9 | 0.95 |
| C10 | 0.188 |
| S | 0.817 |
| O1 | 1.524 |
| O2 | 1.561 |
| N1' | 0.4 |
| C2' | 1.164 |
| CM2 | 2.12 |
| C3' | 1.474 |
| N4' | 1.248 |
| C5' | 1.591 |
| C6' | 1.326 |
3D View
Fluctuation Plot