Difference between revisions of "Molecular Dynamics Simulations Analysis Hemochromatosis"
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==== Total energy ==== |
==== Total energy ==== |
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+ | <figtable id="comparison"> |
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+ | {| class="wikitable" style="float: right; margin: 0 0 0 1em; border: 2px solid darkgray;" cellpadding="0" |
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+ | ! scope="row" align="left" | |
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+ | | align="right" | [[File:Hemo_MD_1a6zC_totalEnergy.png|thumb|300px]] |
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+ | | align="right" | [[File:Hemo_MD_R224W_totalEnergy.png|thumb|300px]] |
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+ | | align="right" | [[File:Hemo_MD_C282S_totalEnergy.png|thumb|300px]] |
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+ | |- |
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+ | |+ style="caption-side: bottom; text-align: left" |<font size=1>'''Table 1:''' different total energies of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S) |
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+ | |} |
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+ | </figtable> |
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Revision as of 18:41, 28 July 2012
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
<figtable id="comparison">
</figtable>
Temperature
<figtable id="comparison">
</figtable>
Potential
<figtable id="comparison">
</figtable>
Total energy
<figtable id="comparison">
</figtable>
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/>