Team:EPF-Lausanne/Analysis

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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 selected>Go to:  </option>
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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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<br>
== Temperature distribution ==
== Temperature distribution ==
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<br><br>
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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<br>
== 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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<br>
==RMSD for individual residues==
==RMSD for individual residues==
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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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<b>This script was highly updated, please go to the [[Team:EPF-Lausanne/Scripts|script page]] if you encounter a problem!!!
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<b>This script was highly updated, please go to the <a href="https://2009.igem.org/Team:EPF-Lausanne/Scripts">script page</a> if you encounter a problem!!!
<br>Selections are not precise here!</b>
<br>Selections are not precise here!</b>
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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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Here is a fast graph of the output of the average RMSD of the atoms in function of time. It seems normal.
Here is a fast graph of the output of the average RMSD of the atoms in function of time. It seems normal.
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<br>[[Image:Rmsd.jpg‎|center]]
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<br><img src="https://static.igem.org/mediawiki/2009/b/bd/Rmsd.jpg">
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Here is what we got with FIRST_FRAME=1115 REFERENCE_FRAME=1115. Average=921.477, standard deviation=202.1708
Here is what we got with FIRST_FRAME=1115 REFERENCE_FRAME=1115. Average=921.477, standard deviation=202.1708
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<br>[[Image:RMSD_plateau.jpg‎|center]]
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<br><img src="https://static.igem.org/mediawiki/2009/2/2c/RMSD_plateau.jpg">
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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
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<br>[[Image:RMSD_COMPLETE_RUN.jpg|center]]
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<br><img src="https://static.igem.org/mediawiki/2009/6/67/RMSD_COMPLETE_RUN.jpg">
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<br>
==Salt bridges==
==Salt bridges==
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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.
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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).
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:ASP471-ARG467
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:GLU409-ARG442
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:FMN450-FMN450
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:'''FMN450-ARG451'''
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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.
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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).
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<br><span style="font-family: Courier;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ASP471-ARG467
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GLU409-ARG442
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;FMN450-FMN450
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ASP540-LYS544
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ASP432-ARG442
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<b>FMN450-ARG451</b>
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GLU457-LYS489
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GLU444-LYS485
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ASP522-ARG521
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ASP424-ARG451
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GLU475-LYS533
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<b>FMN450-ARG467</b></span>
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<br><br>
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.
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[[Image:Salt_bridge.jpg|center]]
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<img src="https://static.igem.org/mediawiki/2009/2/2a/Salt_bridge.jpg">
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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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==RMSF==
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==RMSF==
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After changing the script [see [https://2009.igem.org/Team:EPF-Lausanne/Scripts#RMSF_from_namd_.dcd 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:
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[[Image:Beta_rmsf.jpg|center]]
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If you plot beta factor and RMSF, you get such a thing.
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[[Image:2v02_1ns_rmsf.jpg|center‎]]
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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:
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<br><center><img src="https://static.igem.org/mediawiki/2009/4/4c/Beta_rmsf.jpg"></center>
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<br>If you plot beta factor and RMSF, you get such a thing.
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<img src="https://static.igem.org/mediawiki/2009/7/71/2v02_1ns_rmsf.jpg">
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<br><br>
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

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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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