Difference between revisions of "Molecular Dynamics Simulations Analysis Hemochromatosis"

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=== Energies ===
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==== Pressure ====
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==== Temperature ====
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==== Potential ====
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==== Total energy ====
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=== Minimum distance between periodic boundary cells ===
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=== RMSF for protein and C-alpha ===
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=== Pymol analysis of average and bfactor ===
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=== Radius of gyration ===
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=== solvent accesible surface area ===
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=== hydrogen-bonds between protein and protein / protein and water ===
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=== Ramachandran plots ===
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=== RMSD matrix ===
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=== cluster analysis ===
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=== internal RMSD ===
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Pymol analysis of average and bfactor
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Radius of gyration
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solvent accesible surface area
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hydrogen-bonds between protein and protein / protein and water
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Ramachandran plot: compare it to the standard ramachandran plots. also compare WT and mutations
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RMSD matrix
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cluster analysis
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internal RMSD
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== References ==
  
== References ==

Revision as of 18:26, 28 July 2012

Hemochromatosis>>Task 10: Molecular dynamics simulations analysis


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/>


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