Difference between revisions of "Molecular Dynamcis analysis"

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(Wildtype)
(Wildtype)
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The Simulation tooked ''6h33:50'' ans the simulation speed was ''36.564 ns/day''. So, to reach 1 second of simulation, we had to wait around ''75061'' years. But this is a bit to long for this Project, so we just used the results we got. The potential energy was fluctuating about ''-9.185e+05 kJ/mol'' with a range of about ''0.15e+04 kJ/mol''. These information are given in the different log-files provided by the simulation.
 
The Simulation tooked ''6h33:50'' ans the simulation speed was ''36.564 ns/day''. So, to reach 1 second of simulation, we had to wait around ''75061'' years. But this is a bit to long for this Project, so we just used the results we got. The potential energy was fluctuating about ''-9.185e+05 kJ/mol'' with a range of about ''0.15e+04 kJ/mol''. These information are given in the different log-files provided by the simulation.
   
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|-
 
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{| class="centered"
|[[File:1a6z_wt_cartoon_anim.gif]]
 
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|[[Image:1a6zA.png|thumb|Figure 4 <br> chain 1 of the HFE protein.<br/>Source: http://www.cathdb.info/pdb/1a6z]]
|[File:1a6z_wt_anim.gif]]
 
  +
|[[Image:1a6zB.png|thumb|Figure 5 <br> chain 2 of the HFE protein.<br/>Source: http://www.cathdb.info/pdb/1a6z]]
|-
 
  +
|[[Image:1a6zC.png|thumb|Figure 6 <br> chain 3 of the HFE protein.<br/>Source: http://www.cathdb.info/pdb/1a6z]]
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|[[Image:1a6zD.png|thumb|Figure 7 <br> chain 4 of the HFE protein.<br/>Source: http://www.cathdb.info/pdb/1a6z]]
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|}
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{|
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|[[File:1a6z_wt_cartoon_anim.gif|thumb|Figure 1: Motion of the wildtype protein, Cartoon representation]]
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|[File:1a6z_wt_anim.gif|thumb|Figure 2: Motion of the wildtype protein]]
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|}
   
 
==Mutation 8a [C282Y]==
 
==Mutation 8a [C282Y]==

Revision as of 14:24, 7 September 2011

by Robert Greil and Cedric Landerer

Molecular Dynamics analysis

Wildtype

First of all, we checked the resulting file with gmxcheck.

  • gmxcheck -f ref_md.tpr.xtc

Result

Reading frame       0 time    0.000   
# Atoms  68601
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

The Simulation tooked 6h33:50 ans the simulation speed was 36.564 ns/day. So, to reach 1 second of simulation, we had to wait around 75061 years. But this is a bit to long for this Project, so we just used the results we got. The potential energy was fluctuating about -9.185e+05 kJ/mol with a range of about 0.15e+04 kJ/mol. These information are given in the different log-files provided by the simulation.


Figure 4
chain 1 of the HFE protein.
Source: http://www.cathdb.info/pdb/1a6z
Figure 5
chain 2 of the HFE protein.
Source: http://www.cathdb.info/pdb/1a6z
Figure 6
chain 3 of the HFE protein.
Source: http://www.cathdb.info/pdb/1a6z
Figure 7
chain 4 of the HFE protein.
Source: http://www.cathdb.info/pdb/1a6z
Figure 1: Motion of the wildtype protein, Cartoon representation
thumb|Figure 2: Motion of the wildtype protein]]

Mutation 8a [C282Y]

still waiting to finish // LRZ won't do anything because of LRZ cluster update

Mutation 8b [C282S]

still waiting to finish // LRZ won't do anything because of LRZ cluster update

References

<references />