Difference between revisions of "Molecular Dynamics Simulations Analysis of Glucocerebrosidase"

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(→‎Visualization of results)
(→‎Quality assurance)
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==== Convergence of energy terms ====
  
==== Convergence of energy terms ====
  +
  +
First we look at the energy terms. Therefore we look at the temperature, the pressure, the energy, the volume, the density and the box.
  +
  +
With the following commands we produced *.xvg files which were visualized with xmgrace.
  +
  +
<code>
  +
g_energy -f 2NT0_wt_md.edr -o temperature.xvg<br/>
  +
g_energy -f 2NT0_wt_md.edr -o pressure.xvg<br/>
  +
g_energy -f 2NT0_wt_md.edr -o energy.xvg<br/>
  +
g_energy -f 2NT0_wt_md.edr -o volume.xvg<br/>
  +
g_energy -f 2NT0_wt_md.edr -o density.xvg<br/>
  +
g_energy -f 2NT0_wt_md.edr -o box.xvg
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</code>
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  +
===== Temperature =====
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[[File: glucocerebrosidase_temperature.png|thumb|300px|center|'''Figure 6:''' Temperature of the Molecular Dynamics Simulation of the Wildtype]]
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  +
<code>
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  +
Energy Average Err.Est. RMSD Tot-Drift<br/>
  +
Temperature 297.912 0.0062 1.08924 0.00616934 (K)
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  +
</code>
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  +
===== Pressure =====
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[[File: glucocerebrosidase_pressure.png|thumb|300px|center|'''Figure 7:''' Pressure of the Molecular Dynamics Simulation of the Wildtype]]
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  +
<code>
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Energy Average Err.Est. RMSD Tot-Drift<br/>
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Pressure 1.00032 0.014 87.9016 0.0583997 (bar)
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</code>
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===== Energy =====
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[[File: glucocerebrosidase_energy.png|thumb|300px|center|'''Figure 8:''' Energies of the Molecular Dynamics Simulation of the Wildtype]]
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  +
<code>
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  +
Energy Average Err.Est. RMSD Tot-Drift<br/>
  +
Potential -939801 85 924.013 -583.172 (kJ/mol)<br/>
  +
Kinetic En. 170900 3.6 624.851 3.53909 (kJ/mol)<br/>
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Total Energy -768901 84 1128.21 -579.63 (kJ/mol)
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  +
</code>
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  +
===== Volume =====
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  +
[[File: glucocerebrosidase_volume.png|thumb|300px|center|'''Figure 9:''' Volume of the Molecular Dynamics Simulation of the Wildtype]]
  +
  +
<code>
  +
  +
Energy Average Err.Est. RMSD Tot-Drift<br/>
  +
Volume 735.655 0.042 0.552925 -0.0802412 (nm^3)
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  +
</code>
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  +
===== Density =====
  +
  +
[[File: glucocerebrosidase_density.png|thumb|300px|center|'''Figure 10:''' Density of the Molecular Dynamics Simulation of the Wildtype]]
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  +
<code>
  +
  +
Energy Average Err.Est. RMSD Tot-Drift<br/>
  +
Density 1009.64 0.058 0.75885 0.110104 (kg/m^3)
  +
  +
</code>
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  +
===== Box =====
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  +
[[File: glucocerebrosidase_box.png|thumb|300px|center|'''Figure 11:''' Boxes of the Molecular Dynamics Simulation of the Wildtype]]
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  +
<code>
  +
  +
Energy Average Err.Est. RMSD Tot-Drift<br/>
  +
Box-X 10.1328 0.0002 0.00253864 -0.000368389 (nm)<br/>
  +
Box-Y 10.1328 0.0002 0.00253864 -0.000368389 (nm)<br/>
  +
Box-Z 7.16498 0.00014 0.00179508 -0.000260487 (nm)
  +
  +
</code>
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==== Minimum distances between periodic images ====
  
==== Minimum distances between periodic images ====
 
==== Root mean square fluctuations ====
  
==== Root mean square fluctuations ====

Revision as of 08:22, 23 August 2011

Introduction

To analyze our Molecular Dynamics Simulations we followed the tutorial described here: http://md.chem.rug.nl/~mdcourse/analysis1.html

Wildtype

A brief check of results

  • command: gmxcheck -f 2NT0_wt_md.xtc

How many frames are in the trajectory file and what is the time resolution?

  • 2001 frames
  • timestep: 5ps

How long did the simulation run in real time (hours), what was the simulation speed (ns/day) and how many years would the simulation take to reach a second?

  • Simulation run: 8h37:36
  • Simulation speed: 27.821
  • Time to reach a second: 1/0.000000028 = 35714285,714285714 days = 97847,358121331 years

Which contribution to the potential energy accounts for most of the calculations?

  • -9.39801e+05 kJ/mol

Visualization of results

For visualization we extract 1000 frames from the trajectory (-dt 10), only select the protein without the water and remove the jumps over the boundaries to make a continuous trajectory (-pbc nojump).

  • command: trjconv -s 2NT0_wt_md.tpr -f 2NT0_wt_md.xtc -o protein.pdb -pbc nojump -dt 10
Figure 1: The protein with the spectrum
Figure 2: The protein with the box around it
Figure 3: The cartoon presentation after using the command dss
Figure 4: The active site

STILL MISSING: movie

Quality assurance

Convergence of energy terms

First we look at the energy terms. Therefore we look at the temperature, the pressure, the energy, the volume, the density and the box.

With the following commands we produced *.xvg files which were visualized with xmgrace.

g_energy -f 2NT0_wt_md.edr -o temperature.xvg
g_energy -f 2NT0_wt_md.edr -o pressure.xvg
g_energy -f 2NT0_wt_md.edr -o energy.xvg
g_energy -f 2NT0_wt_md.edr -o volume.xvg
g_energy -f 2NT0_wt_md.edr -o density.xvg
g_energy -f 2NT0_wt_md.edr -o box.xvg

Temperature
Figure 6: Temperature of the Molecular Dynamics Simulation of the Wildtype

Energy Average Err.Est. RMSD Tot-Drift
Temperature 297.912 0.0062 1.08924 0.00616934 (K)

Pressure
Figure 7: Pressure of the Molecular Dynamics Simulation of the Wildtype

Energy Average Err.Est. RMSD Tot-Drift
Pressure 1.00032 0.014 87.9016 0.0583997 (bar)

Energy
Figure 8: Energies of the Molecular Dynamics Simulation of the Wildtype

Energy Average Err.Est. RMSD Tot-Drift
Potential -939801 85 924.013 -583.172 (kJ/mol)
Kinetic En. 170900 3.6 624.851 3.53909 (kJ/mol)
Total Energy -768901 84 1128.21 -579.63 (kJ/mol)

Volume
Figure 9: Volume of the Molecular Dynamics Simulation of the Wildtype

Energy Average Err.Est. RMSD Tot-Drift
Volume 735.655 0.042 0.552925 -0.0802412 (nm^3)

Density
Figure 10: Density of the Molecular Dynamics Simulation of the Wildtype

Energy Average Err.Est. RMSD Tot-Drift
Density 1009.64 0.058 0.75885 0.110104 (kg/m^3)

Box
Figure 11: Boxes of the Molecular Dynamics Simulation of the Wildtype

Energy Average Err.Est. RMSD Tot-Drift
Box-X 10.1328 0.0002 0.00253864 -0.000368389 (nm)
Box-Y 10.1328 0.0002 0.00253864 -0.000368389 (nm)
Box-Z 7.16498 0.00014 0.00179508 -0.000260487 (nm)

Minimum distances between periodic images

Root mean square fluctuations

Convergence of RMSD

Convergence of radius of gyration

Structural analysis: properties derived from configurations

Solvent accessible surface area

Hydrogen bonds

Salt bridges

Secondary structure

Ramachandran (phi/psi) plots

Analysis of dynamics and time-averaged properties

Root mean square deviations again

Cluster analysis

Distance RMSD

Mutation 7

still waiting


Mutation 10

still waiting


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