MD simulation analysis TSD

General

<figtable id="tbl:generalstats">

Table 1: Runtime statistics for the Gromacs simulations. CPU denotes the number of allocated CPUs during the simulation. ns/day and days/s values are based on this number and not normalised.

Model	CPU	Runtime	ns/day	days/s
Wildtype	16	13h52	17.3	3896
R178H	12	19h03	12.6	5354
P182L	32	07h08	33.6	2006

</figtable>

<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.

Thermodynamics

Pressure

<figtable id="tab:pressure">

Table TODO: Pressure oscillations for the three simulations. A cumulative average is shown in red.

	WT, Average:4.077	R178H, Average:1.647	P182L, Average:-0.3182

</figtable>

<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.

Temperature

<figtable id="tab:temperature">

Table TODO: Temperature changes during the simulations. A cumulative average is shown in red.

	WT, Average: 297.9	R178H Average: 297.9	P182L Average: 297.9

</figtable>

<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.

Potential Energy

<figtable id="tab:potentialenergy">

Table TODO: Potential energy changes during the simulations. A cumulative average is shown in red.

	WT Average: -884100	R178H Average: -884100	P182L Average: -884400

</figtable>

<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.

Total Energy

<figtable id="tab:totenergy">

Table TODO: Total energy change during simulations. A cumulative average is shown in red.

	Average: -725700	Average: -725500	Average: -725500

</figtable>

<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.

Flexibility

RMSF

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

Significance

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

References

<references/>