Team:EPF-Lausanne/Analysis

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Revision as of 12:12, 8 September 2009 by Guittet (Talk | contribs)


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

As we wanted to redo the analysis from Schulten's article, we looked for salt bridges. VMD can easily compute this, it even propose an easy GUI. Standard configuration is just fine for now. You'll have a log file containing the list of nitrogen-oxygen susceptible of forming a salt bridge. You'll also get a file for each bridge containing the distance between both atoms along the simulation.

In the light state, we have 9 salt bridges witin the protein and 12 if we consider the protein and the flavin (use "protein or resname FMN" as selection).

ASP471-ARG467
GLU409-ARG442
FMN450-FMN450
ASP540-LYS544
ASP432-ARG442
FMN450-ARG451
GLU457-LYS489
GLU444-LYS485
ASP522-ARG521
ASP424-ARG451
GLU475-LYS533
FMN450-ARG467

Here is a plot for one of the bridges. We have to look for the max distance for a salt bridge.

Salt bridge.jpg


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RMSF

After changing the script [see here], 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:

Beta rmsf.jpg

If you plot beta factor and RMSF, you get such a thing. center‎

This is a 1 nanosecond NPT run at 300°K. We hope to see a RMSF curve identical to the beta factor. It should only be shifted higher because of the increased temperature. But having a similar tendency would mean our simulation show oscillations similar to what was observed during crystallography. This is really a quite nice validation of our run!


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