2-(benzylcarbamoyl-phenylacetylamino-methyl)-5,5-dimethyl-thiazolidine-4-carboxylic acid (hydroxymethyl-2-phenylethyl)amide (G26) 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 | 79 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 3175 |
| 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 | 0.82 | 0.82 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.84 | 0.83 | 0.84 | 0.83 | 0.84 | 0.85 | 0.84 | 0.85 |
| # Exchanges | 4101 | 4101 | 4144 | 4111 | 4091 | 4147 | 4142 | 4185 | 4150 | 4192 | 4168 | 4208 | 4257 | 4197 | 4220 |
| Avg. # Exchanges | 0.82 | 0.82 | 0.83 | 0.82 | 0.82 | 0.83 | 0.83 | 0.84 | 0.83 | 0.84 | 0.83 | 0.84 | 0.85 | 0.84 | 0.84 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 3.0149 | 0.6991 |
| RMSd_exp | 3.9128 | 0.7417 |
| RMSdist_first | 1.9061 | 0.4826 |
| RMSdist_exp | 2.3657 | 0.5220 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.0582 | 0.3738 |
| RgyrX | 4.1276 | 0.3804 |
| RgyrY | 4.3867 | 0.5395 |
| RgyrZ | 3.8260 | 0.3110 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 2.4526 |
| Standard deviation (Å) | 0.9392 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C | 2.474 |
| C1 | 1.531 |
| C2 | 1.424 |
| C3 | 1.244 |
| C4 | 1.289 |
| C5 | 2.925 |
| C6 | 3.502 |
| C7 | 1.186 |
| C8 | 1.608 |
| C9 | 1.859 |
| C10 | 2.665 |
| C11 | 1.661 |
| C12 | 2.016 |
| C13 | 2.465 |
| C14 | 1.927 |
| C15 | 2.45 |
| C16 | 3.106 |
| C17 | 3.322 |
| C18 | 3.12 |
| C19 | 2.209 |
| C20 | 4.797 |
| C21 | 4.403 |
| C22 | 3.386 |
| C23 | 2.68 |
| C24 | 3.315 |
| C25 | 4.342 |
| C26 | 3.242 |
| C27 | 3.441 |
| C28 | 3.184 |
| C29 | 2.478 |
| C30 | 1.925 |
| C31 | 2.528 |
| N | 1.23 |
| N1 | 1.166 |
| N2 | 1.254 |
| N3 | 1.209 |
| O | 1.969 |
| O1 | 1.911 |
| O2 | 2.102 |
| O4 | 3.372 |
| S | 2.641 |
3D View
Fluctuation Plot