Difference between revisions of "Molecular Dynamics Simulations Analysis Hemochromatosis"

From Bioinformatikpedia
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(→‎Calculation statistics)
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GMXcheck revealed for all calculations that all 2001 frames were calculated, resulting in a 10ns model.
  
GMXcheck revealed for all calculations that all 2001 frames were calculated, resulting in a 10ns model.
  +
<!--
  +
GMXCheck:
   
  +
L183P
  +
Checking file scwrl_L183P_md.xtc
  +
Reading frame 0 time 0.000
  +
# Atoms 68613
  +
Precision 0.001 (nm)
  +
Last frame 2000 time 10000.000
  +
  +
  +
Item #frames Timestep (ps)
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Step 2001 5
  +
Time 2001 5
  +
Lambda 0
  +
Coords 2001 5
  +
Velocities 0
  +
Forces 0
  +
Box 2001 5
  +
  +
gcq#11: "She's Not Bad, She's Just Genetically Mean" (Captain Beefheart)
  +
  +
T217I
  +
Checking file scwrl_T217I_md.xtc
  +
Reading frame 0 time 0.000
  +
# Atoms 68614
  +
Precision 0.001 (nm)
  +
Last frame 2000 time 10000.000
  +
  +
  +
Item #frames Timestep (ps)
  +
Step 2001 5
  +
Time 2001 5
  +
Lambda 0
  +
Coords 2001 5
  +
Velocities 0
  +
Forces 0
  +
Box 2001 5
  +
  +
gcq#330: "Go back to the rock from under which you came" (Fiona Apple)
  +
  +
Wildtype
  +
Checking file 1a6zC_md.xtc
  +
Reading frame 0 time 0.000
  +
# Atoms 68607
  +
Precision 0.001 (nm)
  +
Last frame 2000 time 10000.000
  +
  +
  +
Item #frames Timestep (ps)
  +
Step 2001 5
  +
Time 2001 5
  +
Lambda 0
  +
Coords 2001 5
  +
Velocities 0
  +
Forces 0
  +
Box 2001 5
  +
  +
gcq#134: "Push It Real Good" (Salt 'n' Pepa)
  +
  +
C282S
  +
Checking file scwrl_C282S_md.xtc
  +
Reading frame 0 time 0.000
  +
# Atoms 68603
  +
Precision 0.001 (nm)
  +
Last frame 2000 time 10000.000
  +
  +
  +
Item #frames Timestep (ps)
  +
Step 2001 5
  +
Time 2001 5
  +
Lambda 0
  +
Coords 2001 5
  +
Velocities 0
  +
Forces 0
  +
Box 2001 5
  +
  +
gcq#298: "Interfacing Space and Beyond..." (P. J. Harvey)
  +
  +
R224W
  +
Checking file scwrl_R224W_md.xtc
  +
Reading frame 0 time 0.000
  +
# Atoms 68602
  +
Precision 0.001 (nm)
  +
Last frame 2000 time 10000.000
  +
  +
  +
Item #frames Timestep (ps)
  +
Step 2001 5
  +
Time 2001 5
  +
Lambda 0
  +
Coords 2001 5
  +
Velocities 0
  +
Forces 0
  +
Box 2001 5
  +
  +
gcq#236: "Wait a Minute, aren't You.... ? (gunshots) Yeah." (Bodycount)
  +
  +
-->
 
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Revision as of 15:00, 24 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
L183P 13h24:04 17.909 ns/day 152980,4 years
T217I 13h20:12 17.995 ns/day 152249,3 years

</figtable>

GMXcheck revealed for all calculations that all 2001 frames were calculated, resulting in a 10ns model.

References

<references/>


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