[(3s)-6-({2',6'-dimethyl-4'-[3-(methylsulfonyl)propoxy]biphenyl-3-yl}methoxy)-2,3-dihydro-1-benzofuran-3-yl]acetic acid (2YB) 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 | 68 |
| Molecule charge (simulated) | -1 |
| System number of atoms | 4721 |
| 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 | 0.80 | 0.81 | 0.80 | 0.82 | 0.82 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 |
| # Exchanges | 3998 | 4003 | 4006 | 4087 | 4116 | 4091 | 4117 | 4130 | 4117 | 4156 | 4114 | 4140 | 4152 | 4152 | 4210 |
| Avg. # Exchanges | 0.80 | 0.80 | 0.80 | 0.82 | 0.82 | 0.82 | 0.82 | 0.83 | 0.82 | 0.83 | 0.82 | 0.83 | 0.83 | 0.83 | 0.84 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.1732 | 0.7469 |
| RMSd_exp | 2.3069 | 0.8535 |
| RMSdist_first | 1.4828 | 0.9355 |
| RMSdist_exp | 1.5733 | 1.0250 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 6.4149 | 0.7165 |
| RgyrX | 5.8287 | 0.8183 |
| RgyrY | 3.2495 | 0.2152 |
| RgyrZ | 6.1308 | 0.7026 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.9127 |
| Standard deviation (Å) | 0.5712 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C4 | 1.33 |
| C6 | 1.758 |
| C7 | 1.629 |
| C8 | 1.581 |
| C10 | 3.084 |
| C13 | 1.608 |
| C15 | 2.551 |
| C17 | 1.304 |
| C20 | 1.664 |
| C21 | 1.321 |
| C22 | 1.744 |
| C24 | 1.145 |
| C26 | 1.745 |
| C28 | 1.814 |
| C1 | 2.307 |
| C2 | 1.517 |
| C3 | 1.612 |
| O5 | 1.497 |
| S9 | 2.131 |
| O11 | 2.729 |
| O12 | 2.67 |
| C14 | 1.634 |
| C16 | 1.225 |
| C18 | 2.003 |
| C19 | 2.178 |
| O23 | 1.533 |
| C25 | 1.72 |
| C27 | 1.298 |
| C30 | 2.224 |
| C31 | 2.664 |
| O32 | 3.081 |
| O33 | 3.125 |
| C34 | 2.56 |
| O35 | 2.556 |
| C36 | 1.555 |
| C37 | 1.471 |
| C38 | 1.203 |
3D View
Fluctuation Plot