Team:EPF-Lausanne/Analysis

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=Examples=
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=Tutorials=
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<form>
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<tr><td width="100%" background="https://static.igem.org/mediawiki/2009/b/b3/BoxtopA.png"><img border="0" src="11dot.gif" width="19" height="19"></td></tr>
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<tr><td width="2%" background="https://static.igem.org/mediawiki/2009/b/bd/BoxbackA.png">
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</td><td width="98%" background="https://static.igem.org/mediawiki/2009/6/6e/BoxbackB.png">
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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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<p>
<p>
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<a href="javascript:ReverseDisplay('hs1')">Click here to show/hide</a>
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<a href="javascript:ReverseDisplay('hs1')">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Click here to show/hide</a>
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</table>
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<br>
== Energies ==
== Energies ==
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<p>
<p>
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<a href="javascript:ReverseDisplay('hs2')">Click here to show/hide</a>
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<a href="javascript:ReverseDisplay('hs2')">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Click here to show/hide</a>
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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.
<br><br>
<br><br>
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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>
<br><br>
<br><br>
<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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<p>
<p>
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<a href="javascript:ReverseDisplay('hs3')">Click here to show/hide</a>
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<a href="javascript:ReverseDisplay('hs3')">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Click here to show/hide</a>
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</p>
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<br><br>
<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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<p>
<p>
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<a href="javascript:ReverseDisplay('hs4')">Click here to show/hide</a>
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<a href="javascript:ReverseDisplay('hs4')">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Click here to show/hide</a>
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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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<br>
== Pressure as a function of simulation time ==
== Pressure as a function of simulation time ==
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<p>
<p>
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<a href="javascript:ReverseDisplay('hs5')">Click here to show/hide</a>
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<a href="javascript:ReverseDisplay('hs5')">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Click here to show/hide</a>
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</p>
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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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<p>
<p>
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<a href="javascript:ReverseDisplay('hs6')">Click here to show/hide</a>
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<a href="javascript:ReverseDisplay('hs6')">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Click here to show/hide</a>
</p>
</p>
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<li> for the FMN, choose CPK as a drawing method
<li> for the FMN, choose CPK as a drawing method
<li> for the protein, choose tube as drawing method, and <i>user</i> as coloring method. Now click on the Trajectory tab, and in the Color Scale Data Range, type 0.40 and 1.00.
<li> for the protein, choose tube as drawing method, and <i>user</i> as coloring method. Now click on the Trajectory tab, and in the Color Scale Data Range, type 0.40 and 1.00.
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</ul>
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</ul><br><center>
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<br><br><center>
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<img src="https://static.igem.org/mediawiki/2009/thumb/d/dd/Vmd_color.png/200px-Vmd_color.png"></center>
<img src="https://static.igem.org/mediawiki/2009/thumb/d/dd/Vmd_color.png/200px-Vmd_color.png"></center>
<br><br>
<br><br>
The protein is colored according to its average RMSD values. The residues displayed in blue are more mobile while the ones in red move less.  
The protein is colored according to its average RMSD values. The residues displayed in blue are more mobile while the ones in red move less.  
<br><br>
<br><br>
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Here is a movie with the protein colored according to average RMSD values.  
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Here is a movie with the protein colored according to average RMSD values: <a href="https://static.igem.org/mediawiki/2009/4/4d/Moving_residue.mov"> video </a>
<br>
<br>
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[[Media:Moving_residue.mov‎|RMSD moving residues ]]
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<br><br>
<br><br>
<b>5.</b> Now we can plot the RMSD value per residue by typing in a Terminal window :
<b>5.</b> Now we can plot the RMSD value per residue by typing in a Terminal window :
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<br>We obtain the following picture:
<br>We obtain the following picture:
<br>
<br>
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[[Image:RMSD_CA_per_res.jpg‎ | 700px |center]]
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<img src="https://static.igem.org/mediawiki/2009/thumb/c/cc/RMSD_CA_per_res.jpg/700px-RMSD_CA_per_res.jpg">
<br>
<br>
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----
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<hr/>
<p align="center"><big> <b>RMSD of residue within 3 angström of the FMN</b> </big></p>
<p align="center"><big> <b>RMSD of residue within 3 angström of the FMN</b> </big></p>
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[[Image:Resid_3A.jpg | 700px |center]]
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<img src="https://static.igem.org/mediawiki/2009/6/6c/Resid_3A.jpg">
<br><br>
<br><br>
We can see that the residues that move the most are the residue number: 425, 451, 453
We can see that the residues that move the most are the residue number: 425, 451, 453
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<br><br>
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----
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<hr/>
<p align="center"><big> <b>RMSD of residue within 6 angström of the FMN</b> </big></p>
<p align="center"><big> <b>RMSD of residue within 6 angström of the FMN</b> </big></p>
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[[Image:Resid_6A.jpg‎ | 700px |center]]
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<img src="https://static.igem.org/mediawiki/2009/3/3e/Resid_6A.jpg">
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<br>
We can see that the residues that move the most are the residue number:  424, 425, 464, 468
We can see that the residues that move the most are the residue number:  424, 425, 464, 468
<br>
<br>
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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>
  <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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<br>
== RMSD of selected atoms compared to initial position along time ==
== RMSD of selected atoms compared to initial position along time ==
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'''This script was highly updated, please go to the [[Team:EPF-Lausanne/Scripts|script page]] if you encounter a problem!!!'''
 
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'''Selections are not precise here!'''
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<script type="text/javascript" language="JavaScript"><!--
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function ReverseDisplay(d) {
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if(document.getElementById(d).style.display == "none") { document.getElementById(d).style.display = "block"; }
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//--></script>
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<p>
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<a href="javascript:ReverseDisplay('hs7')">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Click here to show/hide</a>
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</p>
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We made a small TCL script to calculate RMSD from selected atoms compared to their initial position along timestep.
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<div id="hs7" style="display:none;">
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The file can be found [[Media:Residue_rmsd_igem09.txt|here.]] Please rename to Residue_rmsd_igem09'''.tcl''' after download.
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<p>
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Example to run the script:
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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!!!
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:load ''.dcd'' + ''.psf'' on VMD
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:source residue_rmsd_igem09.tcl
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:set sel_resid [[atomselect top "protein and alpha"] get resid]
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:rmsd_residue_over_time top $sel_resid 0 0
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We tried to select only backbone from protein + FMN → change
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<br>Selections are not precise here!</b>
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:''set sel_resid [[atomselect top "backbone"] get resid] ''
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<br><br>
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'''The script was updated to be able to define reference frame and first frame were RMSD will be calculated.''' We usually don't need to compute RMSD during heating, for instance. RMSD takes a lot of time. In our first run 1 frame = 100 timesteps * 2 fs*timesteps^-1 = 200 fs
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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 <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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<br><br>
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Example to run the script:
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<br><span style="font-family: Courier;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;load ''.dcd'' + ''.psf'' on VMD
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;source residue_rmsd_igem09.tcl
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;set sel_resid [[atomselect top "protein and alpha"] get resid]
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;rmsd_residue_over_time top $sel_resid 0 0  </span>
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<br><br>
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We tried to select only backbone from protein + FMN → change
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<br><span style="font-family: Courier;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<i>set sel_resid [[atomselect top "backbone"] get resid] </i></span>
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<br><br>
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<b>The script was updated to be able to define reference frame and first frame were RMSD will be calculated.</b> We usually don't need to compute RMSD during heating, for instance. RMSD takes a lot of time. In our first run 1 frame = 100 timesteps * 2 fs*timesteps^-1 = 200 fs
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<br><br>
complete form for run is:
complete form for run is:
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: ''rmsd_residue_over_time top $sel_resid FIRST_FRAME REFERENCE_FRAME''
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<br><span style="font-family: Courier;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <i>rmsd_residue_over_time top $sel_resid FIRST_FRAME REFERENCE_FRAME</i></span>
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<br><br>
For our first run, if we want to select only the 295°K NPT plateau, and set its first frame as reference, we have to launch:
For our first run, if we want to select only the 295°K NPT plateau, and set its first frame as reference, we have to launch:
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: ''rmsd_residue_over_time top $sel_resid 1115 1115''
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<br><span style="font-family: Courier;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<i>rmsd_residue_over_time top $sel_resid 1115 1115</i></span>
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<br><br>
Here is how the script processes:
Here is how the script processes:
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*calculate how many frames are in .dcd
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<ul>
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*for each timestep, the script aligns (best fit) the backbone of the protein to the eference position to minimize RMDS. (Test: "and not mass 1,008000" == and noh was added in selection to remove hydrogen)
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<li>calculate how many frames are in .dcd
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*for each residue (selected by sel_resid), RMSD is computed and the sum of all RMSD (one for each residue) is stored for current timestep
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<li>for each timestep, the script aligns (best fit) the backbone of the protein to the eference position to minimize RMDS. (Test: "and not mass 1,008000" == and noh was added in selection to remove hydrogen)
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*script's output is data_rmsd.dat
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<li>for each residue (selected by sel_resid), RMSD is computed and the sum of all RMSD (one for each residue) is stored for current timestep
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<li>script's output is data_rmsd.dat
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</ul>
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<br><br>
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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[[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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<br><br><br>
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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[[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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<br><br><br>
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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. '''We should compute an average value to normalize amplitude'''. (fluctuation is conserved, anyway) Average=781.3913, standard deviation=118.1393
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[[Image:RMSD_COMPLETE_RUN.jpg|center]]
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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
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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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//--></script>
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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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<p>
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<a href="javascript:ReverseDisplay('hs8')">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Click here to show/hide</a>
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:ASP471-ARG467
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</p>
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:GLU409-ARG442
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:FMN450-FMN450
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:ASP540-LYS544
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:ASP432-ARG442
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:'''FMN450-ARG451'''
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:GLU457-LYS489
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:GLU444-LYS485
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:ASP522-ARG521
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:ASP424-ARG451
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:GLU475-LYS533
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:'''FMN450-ARG467'''
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<div id="hs8" style="display:none;">
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<p>
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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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<br><br>
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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>
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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>
  <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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<br>
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==RMSF==
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<html>
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<script type="text/javascript" language="JavaScript"><!--
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function HideContent(d) {
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document.getElementById(d).style.display = "none";
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}
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function ShowContent(d) {
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document.getElementById(d).style.display = "block";
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function ReverseDisplay(d) {
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<a href="javascript:ReverseDisplay('hs9')">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Click here to show/hide</a>
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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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