N-(2-thienylmethyl)-2,5-thiophenedisulfonamide (TPD) 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 | 29 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1883 |
| 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 | 0.73 | 0.74 | 0.75 | 0.77 | 0.78 | 0.80 | 0.82 | 0.82 | 0.83 | 0.83 | 0.84 | 0.85 | 0.85 | 0.85 | 0.86 |
| # Exchanges | 3672 | 3691 | 3778 | 3844 | 3962 | 4022 | 4081 | 4101 | 4148 | 4207 | 4217 | 4230 | 4240 | 4271 | 4312 |
| Avg. # Exchanges | 0.73 | 0.74 | 0.76 | 0.77 | 0.79 | 0.80 | 0.82 | 0.82 | 0.83 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.86 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.4394 | 0.3818 |
| RMSd_exp | 1.4623 | 0.3063 |
| RMSdist_first | 0.6973 | 0.3273 |
| RMSdist_exp | 0.6494 | 0.2921 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 3.7789 | 0.1976 |
| RgyrX | 3.1000 | 0.1463 |
| RgyrY | 3.3850 | 0.1654 |
| RgyrZ | 2.7359 | 0.1906 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.0400 |
| Standard deviation (Å) | 0.4530 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C3 | 0.488 |
| C9 | 0.879 |
| C10 | 0.572 |
| C11 | 1.493 |
| C12 | 1.528 |
| C13 | 1.003 |
| O1A | 1.493 |
| O2A | 1.5 |
| N21 | 1.532 |
| S1 | 0.492 |
| C4 | 1.7 |
| C5 | 1.75 |
| C6 | 0.571 |
| S2 | 0.84 |
| S7 | 0.448 |
| O3B | 0.748 |
| O4B | 0.8 |
| N8 | 0.615 |
| S14 | 1.308 |
3D View
Fluctuation Plot