Molecular Dynamcis analysis

^{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

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