N-[4-[[glutamic acid]-carbonyl]-benzene-sulfonyl-d-prolinyl]-3-amino-propanoic acid (TP4) 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 | 56 |
| Molecule charge (simulated) | -3 |
| System number of atoms | 2897 |
| 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 | 0.71 | 0.71 | 0.73 | 0.73 | 0.72 | 0.73 | 0.74 | 0.74 | 0.74 | 0.74 | 0.75 | 0.76 | 0.76 | 0.76 | 0.76 |
| # Exchanges | 3544 | 3565 | 3676 | 3681 | 3607 | 3663 | 3664 | 3648 | 3764 | 3675 | 3711 | 3776 | 3777 | 3778 | 3750 |
| Avg. # Exchanges | 0.71 | 0.71 | 0.74 | 0.74 | 0.72 | 0.73 | 0.73 | 0.73 | 0.75 | 0.74 | 0.74 | 0.76 | 0.76 | 0.76 | 0.75 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.6191 | 0.7134 |
| RMSd_exp | 2.7330 | 0.6494 |
| RMSdist_first | 1.4359 | 0.6433 |
| RMSdist_exp | 1.4366 | 0.7154 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.3672 | 0.5123 |
| RgyrX | 5.0619 | 0.6461 |
| RgyrY | 4.9790 | 0.6669 |
| RgyrZ | 2.5926 | 0.3774 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 2.1799 |
| Standard deviation (Å) | 0.7908 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 3.122 |
| C2 | 2.541 |
| N3 | 1.555 |
| C4 | 1.591 |
| C5 | 2.65 |
| C6 | 1.423 |
| O7 | 2.243 |
| N8 | 1.44 |
| S9 | 1.827 |
| C10 | 1.285 |
| O11 | 2.705 |
| O12 | 2.532 |
| C13 | 1.562 |
| C14 | 1.485 |
| C15 | 1.032 |
| C16 | 1.586 |
| C17 | 1.699 |
| C18 | 1.352 |
| N19 | 1.152 |
| C20 | 1.532 |
| C21 | 1.291 |
| C22 | 1.664 |
| C23 | 2.207 |
| O24 | 2.204 |
| C25 | 2.444 |
| O26 | 3.079 |
| O27 | 3.057 |
| O28 | 2.777 |
| O29 | 2.732 |
| C30 | 2.128 |
| C31 | 2.768 |
| C32 | 3.504 |
| O33 | 3.968 |
| O34 | 3.981 |
3D View
Fluctuation Plot