Difference between revisions of "MD simulation analysis TSD"

From Bioinformatikpedia
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=General=
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<div style="float:right; display:inline-block;">
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<figtable id="tbl:generalstats">
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{| class="wikitable", style="width:300px;margin-left:20px; border-collapse: collapse; border-style: solid; border-width:0px; border-color: #000"
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|+ <font size="1"><div align="justify">'''Table 1:''' </div></font>
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|- align="left"
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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" | CPU-Number
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! 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
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! style="border-style: solid; border-width: 0 0 2px 0" | days/s
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|- align="left"
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|| style="border-style: solid; border-width: 0 0 0 0" | Wildtype
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| style="border-style: solid; border-width: 0 0 0 0" | 16
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| style="border-style: solid; border-width: 0 0 0 0" | 13h52
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| style="border-style: solid; border-width: 0 0 0 0" | 17.3
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| style="border-style: solid; border-width: 0 0 0 0" | 3896
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|- align="left"
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| style="border-style: solid; border-width: 0 0 0 0" | R178H
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| style="border-style: solid; border-width: 0 0 0 0" | 12
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| style="border-style: solid; border-width: 0 0 0 0" | 19h03
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| style="border-style: solid; border-width: 0 0 0 0" | 12.6
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| style="border-style: solid; border-width: 0 0 0 0" | 5354
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|- align="left"
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| style="border-style: solid; border-width: 0 0 0 0" | P182L
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| style="border-style: solid; border-width: 0 0 0 0" | 32
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| style="border-style: solid; border-width: 0 0 0 0" | 07h08
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| style="border-style: solid; border-width: 0 0 0 0" | 33.6
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| style="border-style: solid; border-width: 0 0 0 0" | 2006
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|- align="left"
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|}
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</figtable>
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</div>
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<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.
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<br style="clear:both;"/>
 
=Thermodynamics=
 
=Thermodynamics=
 
==Pressure==
 
==Pressure==
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==RMSF==
 
==RMSF==
 
===Significance===
 
===Significance===
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=Conclusion=

Revision as of 16:26, 30 August 2012

General

<figtable id="tbl:generalstats">

Table 1:

Model CPU-Number 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]]
Table TODO: pressure

</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]]
Table TODO: temp

</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]]
Table TODO:potential

</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]]
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