4-[[glutamic acid]-carbonyl]-benzene-sulfonyl-d-proline (TP3) 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 | 46 |
| Molecule charge (simulated) | -3 |
| System number of atoms | 1975 |
| 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 | 0.72 | 0.72 | 0.73 | 0.74 | 0.73 | 0.73 | 0.74 | 0.75 | 0.75 | 0.76 | 0.76 | 0.76 | 0.76 | 0.77 | 0.77 |
| # Exchanges | 3640 | 3608 | 3656 | 3692 | 3648 | 3677 | 3719 | 3767 | 3764 | 3781 | 3768 | 3844 | 3863 | 3827 | 3868 |
| Avg. # Exchanges | 0.73 | 0.72 | 0.73 | 0.74 | 0.73 | 0.74 | 0.74 | 0.75 | 0.75 | 0.76 | 0.75 | 0.77 | 0.77 | 0.77 | 0.77 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.9464 | 0.4110 |
| RMSd_exp | 2.0201 | 0.3796 |
| RMSdist_first | 1.1300 | 0.3071 |
| RMSdist_exp | 0.8842 | 0.2480 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.9237 | 0.2030 |
| RgyrX | 3.8679 | 0.1449 |
| RgyrY | 4.0937 | 0.2319 |
| RgyrZ | 4.0914 | 0.1817 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.4686 |
| Standard deviation (Å) | 0.5676 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 2.876 |
| C2 | 1.934 |
| N3 | 0.743 |
| C4 | 1.197 |
| C5 | 2.428 |
| C6 | 1.402 |
| O7 | 2.019 |
| O8 | 2.054 |
| S9 | 1.03 |
| C10 | 0.911 |
| O11 | 1.868 |
| O12 | 2.004 |
| C13 | 1.49 |
| C14 | 1.457 |
| C15 | 0.829 |
| C16 | 1.463 |
| C17 | 1.483 |
| C18 | 0.859 |
| N19 | 0.555 |
| C20 | 0.576 |
| C21 | 0.742 |
| C22 | 1.126 |
| C23 | 1.481 |
| O24 | 1.423 |
| C25 | 1.09 |
| O26 | 1.742 |
| O27 | 1.687 |
| O28 | 2.028 |
| O29 | 2.091 |
3D View
Fluctuation Plot