Difference between revisions of "MD simulation analysis TSD"

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(→‎Pressure)
(→‎Pressure)
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| align="right" | [[Image:TSD_WT.pressure.xvg.eps.png|thumb|300px|WT]]
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| align="right" | [[Image:TSD_WT.pressure.xvg.eps.png|thumb|300px|WT, Average:4.077]]
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| align="right" | [[Image:TSD_178H.pressure.xvg.eps.png|thumb|300px|R178H]]
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| align="right" | [[Image:TSD_178H.pressure.xvg.eps.png|thumb|300px|R178H, Average:1.647]]
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| align="right" | [[Image:TSD_182L.pressure.xvg.eps.png|thumb|300px|P182L]]
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| align="right" | [[Image:TSD_182L.pressure.xvg.eps.png|thumb|300px|P182L, Average:-0.3182]]
 
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|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table TODO:''' pressure. A cumulative average is shown in red.</div></font>
  
|+ style="caption-side: bottom; text-align: left;" | <font size="1"><div align="justify">'''Table TODO:''' pressure. A cumulative average is shown in red.</div></font>
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<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 undergo any major changes towards the end of the simulations.
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<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.
   
 
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Revision as of 18:48, 30 August 2012

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
style="border-style: solid; border-width: 0 0 0 0" | 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 PP/PME imbalance.


Thermodynamics

Pressure

<figtable id="tab:pressure">

WT, Average:4.077
R178H, Average:1.647
P182L, Average:-0.3182
Table TODO: pressure. A cumulative average is shown in red.

</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:pressure">

TSD WT.temperature.xvg.eps.png
TSD 178H.temperature.xvg.eps.png
TSD 182L.temperature.xvg.eps.png
Table TODO: temp

</figtable>

LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM v LORETEM IPSUM LORETEM IPSUMLORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM v LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM v LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM



Potential

<figtable id="tab:pressure">

TSD WT.potential.xvg.eps.png
TSD 178H.potential.xvg.eps.png
TSD 182L.potential.xvg.eps.png
Table TODO:potential

</figtable>

LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM v LORETEM IPSUM LORETEM IPSUMLORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM v LORETEM IPSUM LORETEM IPSUMLORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM v LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM

Total Energy

LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM v LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM

<figtable id="tab:pressure">

TSD WT.totalEnergy.xvg.eps.png
TSD 178H.totalEnergy.xvg.eps.png
TSD 182L.totalEnergy.xvg.eps.png
Table TODO: total energy

</figtable>


LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM v LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM

Flexibility

RMSF

Significance

Conclusion

References

<references/>

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