Difference between revisions of "Canavan Task 10 - Molecular Dynamics Simulations"

From Bioinformatikpedia
(Temperature)
(Pressure)
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===Pressure===
 
===Pressure===
 
   
   
 
<figtable id="energies_temp">
 
<figtable id="energies_temp">
 
<table cellspacing=0 align="center" cellpadding=5>
 
<table cellspacing=0 align="center" cellpadding=5>
<caption align="center"><b><xr nolink id="energies_temp"/></b> Results from gmxcheck and the logfile</caption>
+
<caption align="center"><b><xr nolink id="energies_temp"/></b> Quality check for convergence of energy values: temperature.</caption>
   
 
<tr>
 
<tr>
Line 172: Line 171:
 
</figtable>
 
</figtable>
   
  +
===Potential Energy ===
   
  +
<figtable id="energies_potential">
  +
<table cellspacing=0 align="center" cellpadding=5>
  +
<caption align="center"><b><xr nolink id="energies_potential"/></b> Quality check for convergence of energy values: potential energy.</caption>
   
  +
<tr>
  +
<td style="border-bottom:solid;border-right:solid;" align="center"></td>
  +
<td style="border-bottom:solid;border-right:solid;" align="center">WT </td>
  +
<td style="border-bottom:solid;border-right:solid;" align="center">K213E </td>
  +
<td style="border-bottom:solid;border-right:solid;" align="center">A305E </td>
  +
</tr>
   
<table>
 
 
<tr>
 
<tr>
  +
<td style="border-right:solid;" align="center">Reference Value</td>
<td>Energy</td>
 
  +
<td style="border-right:solid;" align="center"> </td>
<td>Reference value</td>
 
  +
<td style="border-right:solid;" align="center"> </td>
<td>Average</td>
 
  +
<td style="border-right:solid;" align="center" > </td>
<td>Err.Est.</td>
 
<td>RMSD</td>
 
<td>Tot-Drift</td>
 
<td>Plot</td>
 
 
</tr>
 
</tr>
   
  +
<tr>
  +
<td style="border-right:solid;" align="center">Average</td>
  +
<td style="border-right:solid;" align="center">-592161</td>
  +
<td style="border-right:solid;" align="center"> </td>
  +
<td style="border-right:solid;" align="center" > </td>
  +
</tr>
  +
  +
<tr>
  +
<td style="border-right:solid;" align="center">Err.Est.</td>
  +
<td style="border-right:solid;" align="center">55 </td>
  +
<td style="border-right:solid;" align="center"> </td>
  +
<td style="border-right:solid;" align="center" > </td>
  +
</tr>
   
   
 
<tr>
 
<tr>
  +
<td style="border-right:solid;" align="center">RMSD</td>
<td>Potential</td>
 
  +
<td style="border-right:solid;" align="center"> 721.947</td>
<td></td>
 
  +
<td style="border-right:solid;" align="center"> </td>
<td>-592161</td>
 
  +
<td style="border-right:solid;" align="center" > </td>
<td>55</td>
 
<td>721.947</td>
 
<td>-252.112 (kJ/mol)</td>
 
<td><figure id="wt_potential">[[File:CD_wt_potential.png|thumb|200px|<b><xr nolink id="wt_potential"/></b></br>]]</figure></td>
 
 
</tr>
 
</tr>
  +
   
 
<tr>
 
<tr>
  +
<td style="border-right:solid;" align="center">Total Drift</td>
<td> Total Energy </td>
 
  +
<td style="border-right:solid;" align="center"> -252.112 (kJ/mol) </td>
<td></td>
 
  +
<td style="border-right:solid;" align="center"> </td>
<td>-485680</td>
 
  +
<td style="border-right:solid;" align="center" > </td>
<td>54</td>
 
<td>886.726</td>
 
<td>-252.262 (kJ/mol)</td>
 
<td><figure id="wt_tot_energy">[[File:CD_wt_tot_energy.png|thumb|200px|<b><xr nolink id="wt_tot_energy"/></b></br>]]</figure></td>
 
 
</tr>
 
</tr>
  +
  +
<tr>
  +
<td style="border-right:solid;" align="center">Plot</td>
  +
<td style="border-right:solid;" align="center"><figure id="wt_potential">[[File:CD_wt_potential.png|thumb|200px|<b><xr nolink id="wt_potential"/></b></br>]]</figure></td>
  +
<td style="border-right:solid;" align="center"> </td>
  +
<td style="border-right:solid;" align="center" > </td>
  +
</tr>
  +
  +
  +
</table>
  +
</figtable>
  +
  +
  +
===Total energy===
  +
  +
<figtable id="energies_total">
  +
<table cellspacing=0 align="center" cellpadding=5>
  +
<caption align="center"><b><xr nolink id="energies_total"/></b> Quality check for convergence of energy values: total energy.</caption>
  +
  +
<tr>
  +
<td style="border-bottom:solid;border-right:solid;" align="center"></td>
  +
<td style="border-bottom:solid;border-right:solid;" align="center">WT </td>
  +
<td style="border-bottom:solid;border-right:solid;" align="center">K213E </td>
  +
<td style="border-bottom:solid;border-right:solid;" align="center">A305E </td>
  +
</tr>
  +
  +
<tr>
  +
<td style="border-right:solid;" align="center">Reference Value</td>
  +
<td style="border-right:solid;" align="center"> </td>
  +
<td style="border-right:solid;" align="center"> </td>
  +
<td style="border-right:solid;" align="center" > </td>
  +
</tr>
  +
  +
<tr>
  +
<td style="border-right:solid;" align="center">Average</td>
  +
<td style="border-right:solid;" align="center">-485680</td>
  +
<td style="border-right:solid;" align="center"> </td>
  +
<td style="border-right:solid;" align="center" > </td>
  +
</tr>
  +
  +
<tr>
  +
<td style="border-right:solid;" align="center">Err.Est.</td>
  +
<td style="border-right:solid;" align="center">54 </td>
  +
<td style="border-right:solid;" align="center"> </td>
  +
<td style="border-right:solid;" align="center" > </td>
  +
</tr>
  +
  +
  +
<tr>
  +
<td style="border-right:solid;" align="center">RMSD</td>
  +
<td style="border-right:solid;" align="center"> 886.726</td>
  +
<td style="border-right:solid;" align="center"> </td>
  +
<td style="border-right:solid;" align="center" > </td>
  +
</tr>
  +
  +
  +
<tr>
  +
<td style="border-right:solid;" align="center">Total Drift</td>
  +
<td style="border-right:solid;" align="center"> -252.262 (kJ/mol) </td>
  +
<td style="border-right:solid;" align="center"> </td>
  +
<td style="border-right:solid;" align="center" > </td>
  +
</tr>
  +
  +
<tr>
  +
<td style="border-right:solid;" align="center">Plot</td>
  +
<td style="border-right:solid;" align="center"><figure id="wt_tot_energy">[[File:CD_wt_tot_energy.png|thumb|200px|<b><xr nolink id="wt_tot_energy"/></b></br>]]</figure></td>
  +
<td style="border-right:solid;" align="center"> </td>
  +
<td style="border-right:solid;" align="center" > </td>
  +
</tr>
  +
   
 
</table>
 
</table>

Revision as of 15:00, 28 July 2012

Protocol

Further information and commands can be found in the protocol.

Initial Checks

For all three runs, there are 2000 time frames, with a resolution of 5 psec. Therefore the whole simulation ran for 10000 psec = 10 nsec.

<figtable id="gmxcheck">

<xr nolink id="gmxcheck"/> Results from gmxcheck and the logfile
WT K213E A305E
run time 5h 22:37 5h 08:54 5h 08:35
atoms outside of box 406, 408, 480, 482, 483, 484, 485, 486, 500, 501,.. 406, 480, 482, 483, 484, 485, 486, 500, 502, 503,.. 406, 408, 480, 482, 483, 484, 485, 486, 500, 501,..
Last frame 2000 time 10000.000 2000 time 10000.000 2000 time 10000.000

</figtable>

Energies

For all analysed thermodynamical parameters convergence could be observed. Though, for pressure the values vary enormously, but the average pressure is close to the specified value of 1 bar.

Temperature

<figtable id="energies_temp">

<xr nolink id="energies_temp"/> Quality check for convergence of energy values: temperature.
WT K213E A305E
Reference Value 298 K
Average 297.914 K
Err.Est. 0.0072
RMSD 1.38693
Total Drift -0.00042403 (K)
Plot <figure id="wt_temp">
<xr nolink id="wt_temp"/>
</figure>

</figtable>

Pressure

<figtable id="energies_temp">

<xr nolink id="energies_temp"/> Quality check for convergence of energy values: temperature.
WT K213E A305E
Reference Value 1.0 (Berendsen barostat)
Average 1.00763
Err.Est. 0.018
RMSD 111.943
Total Drift -0.0713928 (bar)
Plot <figure id="wt_pressure">
<xr nolink id="wt_pressure"/>
</figure>

</figtable>

Potential Energy

<figtable id="energies_potential">

<xr nolink id="energies_potential"/> Quality check for convergence of energy values: potential energy.
WT K213E A305E
Reference Value
Average -592161
Err.Est. 55
RMSD 721.947
Total Drift -252.112 (kJ/mol)
Plot <figure id="wt_potential">
<xr nolink id="wt_potential"/>
</figure>

</figtable>


Total energy

<figtable id="energies_total">

<xr nolink id="energies_total"/> Quality check for convergence of energy values: total energy.
WT K213E A305E
Reference Value
Average -485680
Err.Est. 54
RMSD 886.726
Total Drift -252.262 (kJ/mol)
Plot <figure id="wt_tot_energy">
<xr nolink id="wt_tot_energy"/>
</figure>

</figtable>

distances between periodic boundaries

The shortest periodic distance is 1.6456 (nm) at time 7675 (ps), between atoms 15 and 4507.

As expected the minimum distance to periodic images is larger when only considering C-alpha atoms, than for the whole protein with all sidechains. The suggested distance limit of 2nm is undercut for at some timesteps during the simulation.

<figtable id="wt_pi">

<figure id="wt_pi_ca">
<xr nolink id="wt_pi_ca"/>
</figure>
<figure id="wt_pi">
<xr nolink id="wt_pi"/>
</figure>

</figtable>

RMSF

Only small fluctuations can be observed for the residues of the wildtype protein. There is a region between residues 120 and 180 that is especially rigid.

When looking at the bfactors one finds the same results. The whole protein is rather rigid and only some exposed loops have higher bfactors.

For exposed residues the averaged structure shows several possible residue conformers.

<figtable id="wt_rmsf">

<figure id="wt_rmsf_plot">
<xr nolink id="wt_rmsf_plot"/>
</figure>
<figure id="wt_bfactors">
<xr nolink id="wt_bfactors"/>
</figure>
<figure id="wt_average">
<xr nolink id="wt_average"/>
</figure>

</figtable>

Convergence of RMSD

As expected, the RMSD increases when using the starting structure as a reference. Over the simulation the structure changes and deviates more and more from the starting structure. Yet these changes are not tremendous, as the starting structure is the crystal structure and therefore should already have adopted a optimal conformation.

When taking the average structure as reference, the RMSD is higher at the beginning of the simulation and finally converges as the structure reaches an equilibrium.

When only taking the Calpha atoms into accounts, the deviations are even smaller, than when also calculating RMSD values for the flexible side chains.


<figtable id="CD_wt_rmsf">

<figure id="wt_rmsd_all_vs_first">
<xr nolink id="wt_rmsd_all_vs_first"/>
</figure>
<figure id="wt_rmsd_all_vs_average">
<xr nolink id="wt_rmsd_all_vs_average"/>
</figure>
<figure id="wt_rmsd_calpha_vs_first">
<xr nolink id="wt_rmsd_calpha_vs_first"/>
</figure>
<figure id="wt_rmsd_calpha_vs_average">
<xr nolink id="wt_rmsd_calpha_vs_average"/>
</figure>

</figtable>


Radius of gyration

Against our expectations, the radius of gyration increases for the wildtype protein. As the energy of the system decreases during hte rund, we would expect that the protein becomes more compact. One idea is, that we used the monomeric form of the protein for the simulation, whereas in the crystal structure it is a dimer.


<figure id="wt_rg">

<xr nolink id="wt_rg"/>

</figure>