Difference between revisions of "Molecular Dynamcis analysis"
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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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| − | |[[Image:1a6zA.png|thumb|Figure 4 <br> chain 1 of the HFE protein.<br/>Source: http://www.cathdb.info/pdb/1a6z]] |
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| − | |[[Image:1a6zB.png|thumb|Figure 5 <br> chain 2 of the HFE protein.<br/>Source: http://www.cathdb.info/pdb/1a6z]] |
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| − | |[[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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Revision as of 14:25, 7 September 2011
by Robert Greil and Cedric Landerer
Contents
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.
| 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 />
