Team:EPF-Lausanne/Analysis

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=Tutorials=
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<select class="combobox" name="SiteMap" onchange="if(options[selectedIndex].value){location = options[selectedIndex].value}" size="1">
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<option value="https://2009.igem.org/Team:EPF-Lausanne/Analysis#Maxwell-Boltzmann_Energy_Distribution">Maxwell-Boltzmann Energy Distribution </option><option value="https://2009.igem.org/Team:EPF-Lausanne/Analysis#Energies">Energies</option><option value="https://2009.igem.org/Team:EPF-Lausanne/Analysis#Temperature_distribution">Temperature distribution</option><option value="https://2009.igem.org/Team:EPF-Lausanne/Analysis#Density">Density </option><option value="https://2009.igem.org/Team:EPF-Lausanne/Analysis#Pressure_as_a_function_of_simulation_time">Pressure</option><option value="https://2009.igem.org/Team:EPF-Lausanne/Analysis#RMSD_for_individual_residues">RMSD for individual residues</option><option value="https://2009.igem.org/Team:EPF-Lausanne/Analysis#RMSD_of_selected_atoms_compared_to_initial_position_along_time">RMSD of selected atoms</option><option value="https://2009.igem.org/Team:EPF-Lausanne/Analysis#Salt_bridges">Salt bridges</option><option value="https://2009.igem.org/Team:EPF-Lausanne/Analysis#RMSF">RMSF</option>
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== Maxwell-Boltzmann Energy Distribution ==
== Maxwell-Boltzmann Energy Distribution ==
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== Energies ==
== Energies ==
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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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== Temperature distribution ==
== Temperature distribution ==
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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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== Density ==
== Density ==
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<br><center><img src="https://static.igem.org/mediawiki/2009/e/e7/Density.jpg"></center>
<br><center><img src="https://static.igem.org/mediawiki/2009/e/e7/Density.jpg"></center>
<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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== Pressure as a function of simulation time ==
== Pressure as a function of simulation time ==
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Here is a small plot of pressure and temperature in function of time
Here is a small plot of pressure and temperature in function of time
<img src="https://static.igem.org/mediawiki/2009/f/f9/1st_run.jpg">
<img src="https://static.igem.org/mediawiki/2009/f/f9/1st_run.jpg">
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==RMSD for individual residues==
==RMSD for individual residues==
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  <p align="center" class="style1"><a href="#top"><img src="https://static.igem.org/mediawiki/2009/thumb/0/06/Up_arrow.png/50px-Up_arrow.png" alt="Back to top" border="0"></a><br></p>
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== RMSD of selected atoms compared to initial position along time ==
== RMSD of selected atoms compared to initial position along time ==
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We made a small TCL script to calculate RMSD from selected atoms compared to their initial position along timestep.
We made a small TCL script to calculate RMSD from selected atoms compared to their initial position along timestep.
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The file can be found [[Media:Residue_rmsd_igem09.txt|here.]] Please rename to Residue_rmsd_igem09<b>.tcl</b> after download.
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The file can be found <a href="https://static.igem.org/mediawiki/2009/a/ad/Residue_rmsd_igem09.txt">here</a>. Please rename to Residue_rmsd_igem09<b>.tcl</b> after download.
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Example to run the script:
Example to run the script:
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FIRST_FRAME=0 REFERENCE_FRAME=0. The difference of the sum probably comes from the new selection of atoms from the backbone. <b>We should compute an average value to normalize amplitude</b>. (fluctuation is conserved, anyway) Average=781.3913, standard deviation=118.1393
FIRST_FRAME=0 REFERENCE_FRAME=0. The difference of the sum probably comes from the new selection of atoms from the backbone. <b>We should compute an average value to normalize amplitude</b>. (fluctuation is conserved, anyway) Average=781.3913, standard deviation=118.1393
<br><img src="https://static.igem.org/mediawiki/2009/6/67/RMSD_COMPLETE_RUN.jpg">
<br><img src="https://static.igem.org/mediawiki/2009/6/67/RMSD_COMPLETE_RUN.jpg">
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==Salt bridges==
==Salt bridges==
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Here is a plot for one of the bridges. We have to look for the max distance for a salt bridge.
Here is a plot for one of the bridges. We have to look for the max distance for a salt bridge.
<img src="https://static.igem.org/mediawiki/2009/2/2a/Salt_bridge.jpg">
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==RMSF==
==RMSF==
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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!
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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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

         Click here to show/hide


Energies

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Temperature distribution

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Density

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Pressure as a function of simulation time

         Click here to show/hide


RMSD for individual residues

         Click here to show/hide


RMSD of selected atoms compared to initial position along time

         Click here to show/hide


Salt bridges

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RMSF

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