Molecular Dynamcis analysis

^{by Robert Greil and Cedric Landerer}

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 1: Motion of the wildtype protein, Cartoon representation

Figure 2: Motion of the wildtype protein

To create the images, we saved each frame in PyMol<ref>The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC</ref> as an image, which we converted into gif format by

• for file in *.png; do convert "$file" "$(basename $file .png).gif"; done.

Than we were able to use gifsicle to create an animated gif.

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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