Molecular Dynamics Simulations Analysis Hemochromatosis
From Bioinformatikpedia
Hemochromatosis>>Task 10: Molecular dynamics simulations analysis
Contents
- 1 Short task description
- 2 Protocol
- 3 Dummy
- 3.1 Calculation statistics
- 3.2 Energies
- 3.3 Minimum distance between periodic boundary cells
- 3.4 RMSF for protein and C-alpha
- 3.5 Pymol analysis of average and bfactor
- 3.6 Radius of gyration
- 3.7 solvent accesible surface area
- 3.8 hydrogen-bonds between protein and protein / protein and water
- 3.9 Ramachandran plots
- 3.10 RMSD matrix
- 3.11 cluster analysis
- 3.12 internal RMSD
- 4 References
Short task description
Detailed description: Molecular dynamics simulations analysis
Protocol
A protocol with a description of the data acquisition and other scripts used for this task is available here.
Dummy
Calculation statistics
<figtable id="tab:simulation_stats"> Statistics of the MD simulations
| Input | Calc. time | Calc. speed | time to reach 1 s |
|---|---|---|---|
| Wildtype | 13h31:15 | 17.750 ns/day | 154350,8 years |
| C282S | 13h35:05 | 17.667 ns/day | 155075,9 years |
| R224W | 13h35:02 | 17.668 ns/day | 155067,1 years |
</figtable>
GMXcheck revealed for all calculations that all 2001 frames were calculated, resulting in a 10ns model.
Energies
Pressure
Temperature
Potential
Total energy
Minimum distance between periodic boundary cells
RMSF for protein and C-alpha
Pymol analysis of average and bfactor
Radius of gyration
solvent accesible surface area
hydrogen-bonds between protein and protein / protein and water
Ramachandran plots
RMSD matrix
cluster analysis
internal RMSD
References
<references/>
