Cholic acid (CHD) 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 | 1988 |
| 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 | 0.81 | 0.82 | 0.82 | 0.82 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.85 |
| # Exchanges | 4070 | 4081 | 4064 | 4091 | 4094 | 4092 | 4138 | 4095 | 4189 | 4193 | 4129 | 4214 | 4238 | 4229 | 4239 |
| Avg. # Exchanges | 0.81 | 0.82 | 0.81 | 0.82 | 0.82 | 0.82 | 0.83 | 0.82 | 0.84 | 0.84 | 0.83 | 0.84 | 0.85 | 0.85 | 0.85 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 0.6493 | 0.2854 |
| RMSd_exp | 0.6486 | 0.2885 |
| RMSdist_first | 0.3260 | 0.1358 |
| RMSdist_exp | 0.3329 | 0.1400 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.3669 | 0.0944 |
| RgyrX | 3.7893 | 0.1024 |
| RgyrY | 2.7628 | 0.0332 |
| RgyrZ | 4.0181 | 0.0939 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 0.4246 |
| Standard deviation (Å) | 0.2993 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.255 |
| C2 | 0.323 |
| C3 | 0.381 |
| O3 | 0.54 |
| C4 | 0.293 |
| C5 | 0.203 |
| C6 | 0.196 |
| C7 | 0.193 |
| O7 | 0.3 |
| C8 | 0.17 |
| C9 | 0.126 |
| C10 | 0.162 |
| C11 | 0.213 |
| C12 | 0.282 |
| O12 | 0.378 |
| C13 | 0.301 |
| C14 | 0.269 |
| C15 | 0.371 |
| C16 | 0.463 |
| C17 | 0.412 |
| C18 | 0.35 |
| C19 | 0.291 |
| C20 | 0.498 |
| C21 | 0.541 |
| C22 | 0.639 |
| C23 | 0.726 |
| O25 | 1.362 |
| C24 | 0.71 |
| O26 | 1.364 |
3D View
Fluctuation Plot