Difference between revisions of "MD simulation analysis TSD"
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<figtable id="tbl:generalstats"> |
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| − | |+ <font size="1"><div align="justify">'''Table 1:''' </div></font> |
+ | |+ <font size="1"><div align="justify">'''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.</div></font> |
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! style="border-style: solid; border-width: 0 0 2px 0" | Model |
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! style="border-style: solid; border-width: 0 0 2px 0" | Runtime |
! style="border-style: solid; border-width: 0 0 2px 0" | Runtime |
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! style="border-style: solid; border-width: 0 0 2px 0" | ns/day |
! style="border-style: solid; border-width: 0 0 2px 0" | ns/day |
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=Thermodynamics= |
=Thermodynamics= |
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==Pressure== |
==Pressure== |
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Revision as of 16:31, 30 August 2012
Contents
General
<figtable id="tbl:generalstats">
| 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
LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM 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 IPSUM LORETEM IPSUM LORETEM IPSUMLORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM LORETEM IPSUM vLORETEM 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 IPSUM LORETEM IPSUMLORETEM IPSUM <figtable id="tab:pressure">
| [[Image:|thumb|300px]] | [[Image:|thumb|300px]] | [[Image:|thumb|300px]] |
</figtable>
Temperature
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 <figtable id="tab:pressure">
| [[Image:|thumb|300px]] | [[Image:|thumb|300px]] | [[Image:|thumb|300px]] |
</figtable>
Potential
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 <figtable id="tab:pressure">
| [[Image:|thumb|300px]] | [[Image:|thumb|300px]] | [[Image:|thumb|300px]] |
</figtable>
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">
| [[Image:|thumb|300px]] | [[Image:|thumb|300px]] | [[Image:|thumb|300px]] |
</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
