MD simulation analysis TSD
<xr id="tbl:generalstats"/> shows general statistics about the three simulations. It should be noted that the output of gmxcheck does not account for the number of CPUs used in the calculation and only reports the real time that passed. Normalizing the runtimes by the number of CPUs involved yields that the Wildtype and P182L mutation completed within 4 hours. R178H took 4 hours longer, however the difference is negligible, considering that they were not done in a testing environment and it is assumed that all CPUs could maintain equal load throughout the runs. In fact Gromacs reports a particularly high 12% of the time being lost due to particle-particle/Particle-Mesh-Ewald imbalance.
<xr id="tab:pressure"/> shows the pressure oscillations for the three simulations. As can be seen per-frame values differ by several 100 bar, as to be expected <ref name="gromacsmanualpressure">http://www.gromacs.org/Documentation/Terminology/Pressure</ref>. More importantly the average shows convergence in every simulation and does not undergo any major changes towards the end of the simulations. The final average pressure also lies close to 0 in all cases.
<xr id="tab:temperature"/> shows the temperature variances during the simulations. The mutations both show higher extreme values than the wildtype structure, especially P182L. The average however remains exactly the same for all simulations, which is the expected behavior after a period of time passed <ref name="">http://www.gromacs.org/Documentation/Terminology/Thermostats</ref>. The fact the all simulations arrive at the same value also supports that the simulations went well and arrived at the correct temperature.
<xr id="tab:potentialenergy"/> shows the fluctuations of potential energy during the simulations. As can be seen, during all simulations it is globally decreasing and the final averages of all three runs are similar.
<xr id="tab:totenergy"/> shows the total energy which is composed of the potential energy shown before and the kinetic energy <ref name="gromacstotenergy">http://www.gromacs.org/Documentation/Terminology/Total_Energy</ref>. It also globally decreases for all runs and the final averages are very similar which leads to the conclusion, that the kinetic energy behaves similarly. Given that the WT behaves in the same way than the mutations one cannot say that the mutations have an effect on the total energy.
Comparison with B-Factors
b-factor ca gg. prot -- 3x should be pretty much the same so in the following we only look at the prot one
now check how avg (i.e. rmsf which is per residue mean movement), behaves compared to the b-factor this is probably also comparable?
wenn nein, prima. dann final nochmal B-factors von prot von den mutationen verglichen mit dem aus dem wildtype. soll heissen, aendern unsere mutationen irgendetwas daran wie sich das ding verhael in terms of flexibility?
look at b-factors in the very original file, that is the experimentally annotated ones. especially how are they in the domain that we cut out?
RMS Fluctuation plots
this is the flucutation of the atom around its average. depending on above it should be ok, if we only show prot! or simply see again manually, whether they look similar
marcos pi test anschaun see pku
RMSD against average
is that really it?
THESE ARE a different topci!! see CONVERGENCE OF RMSD
in manual! (probably different)
RMSD against start
and probably end as well? check again