Team:EPF-Lausanne/Analysis

From 2009.igem.org

(Difference between revisions)
(RMSF)
(RMSF)
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After changing the script [see <a href="https://2009.igem.org/Team:EPF-Lausanne/Scripts#RMSF_from_namd_.dcd"> here</a>], we perform an interesting analysis from these 2 files. First, we have to correct the RMSF, that can be linked to beta factor using this equation:
After changing the script [see <a href="https://2009.igem.org/Team:EPF-Lausanne/Scripts#RMSF_from_namd_.dcd"> here</a>], we perform an interesting analysis from these 2 files. First, we have to correct the RMSF, that can be linked to beta factor using this equation:
-
<br><img src="https://static.igem.org/mediawiki/2009/4/4c/Beta_rmsf.jpg">
+
<br><center><img src="https://static.igem.org/mediawiki/2009/4/4c/Beta_rmsf.jpg"></center>
<br>If you plot beta factor and RMSF, you get such a thing.
<br>If you plot beta factor and RMSF, you get such a thing.
<img src="https://static.igem.org/mediawiki/2009/7/71/2v02_1ns_rmsf.jpg">
<img src="https://static.igem.org/mediawiki/2009/7/71/2v02_1ns_rmsf.jpg">

Revision as of 12:21, 8 September 2009


Analysis of Equilibrium





Scripts

As this page is getting crowded, we created another page to explain all the scripts we wrote. The current page has some kind of step by step tutorials, but if you want fast informations, you better go to the script page.


Examples

Maxwell-Boltzmann Energy Distribution

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Energies

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Temperature distribution

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Density

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Pressure as a function of simulation time

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RMSD for individual residues

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RMSD of selected atoms compared to initial position along time

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Salt bridges

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RMSF

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