Difference between revisions of "Molecular Dynamics Simulations Analysis Hemochromatosis"

Revision as of 18:36, 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

**Table 1:** different pressures of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutatuin at position 282 (C282S)

</figtable>

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

@@ Line 165: / Line 165: @@
 === Energies ===
 ==== Pressure ====
+<figtable id="comparison">
+{|  class="wikitable"  style="float: right; margin: 0 0 0 1em; border: 2px solid darkgray;"   cellpadding="0"
+!  scope="row" align="left" |
+|  align="right" | [[File:Hemo_MD_1a6zC_pressure.png|thumb|300px]]
+|  align="right" | [[File:Hemo_MD_R224W_pressure.png|thumb|300px]]
+|  align="right" | [[File:Hemo_MD_C282S_pressure.png|thumb|300px]]
+|-
+|+ style="caption-side: bottom; text-align: left" |<font size=1>'''Table 1:''' different pressures of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutatuin at position 282 (C282S)
+|}
+</figtable>
 <br style="clear:both;">