Team:EPF-Lausanne/Analysis

From 2009.igem.org

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== Maxwell-Boltzmann Energy Distribution ==
== Maxwell-Boltzmann Energy Distribution ==
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angles and dihedrals) and non-bonded (electrostatic, van der Waals)) over the course of a simulation.
angles and dihedrals) and non-bonded (electrostatic, van der Waals)) over the course of a simulation.
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<b>1.</b> We start with a file obtained from NAMD: http://www.ks.uiuc.edu/Research/namd/utilities/ and download <i>namdstat.tcl</i>
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<b>1.</b> We start with a file obtained from NAMD: <br>http://www.ks.uiuc.edu/Research/namd/utilities/ and download <i>namdstat.tcl</i>
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<b>2.</b> In the VMD TkCon window, type :
<b>2.</b> In the VMD TkCon window, type :
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Using EXCEL, we obtain the following graph, which represents the evolution of the temperature in function of time:
Using EXCEL, we obtain the following graph, which represents the evolution of the temperature in function of time:
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<br><img src="https://static.igem.org/mediawiki/2009/c/cf/Temp%28t%29.png">
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<br><br><img src="https://static.igem.org/mediawiki/2009/c/cf/Temp%28t%29.png">
<br>The first part corresponds the the heating, then we let the system reach an equilibrium (NPT state), a NVT portion, and finally a NPT portion again.
<br>The first part corresponds the the heating, then we let the system reach an equilibrium (NPT state), a NVT portion, and finally a NPT portion again.
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Latest revision as of 09:21, 21 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.


Tutorials


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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