Molecular Dynamics Analysis GLA

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by Benjamin Drexler and Fabian Grandke

Introduction

In this task we analysed the simulated data that have been created within task 8. We used several tools of GROMACS to analyse the data and Pymol to visualize them.

Methods/Materials

Results

Wildtype

Brief check of the results

Visualization of the results

Quality assurance

Convergence of energy terms

Interaction Energy: Coulomb

Interaction Energy: Van der Waals

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

Ramachandran (phi/psi) plots=

Analysis of dynamics and time-averaged properties

Root mean square deviations again

Cluster analysis

Distance RMSD

Mutation 3

Brief check of the results

Visualization of the results

Quality assurance

Convergence of energy terms

Interaction Energy: Coulomb

Interaction Energy: Van der Waals

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

Ramachandran (phi/psi) plots=

Analysis of dynamics and time-averaged properties

Root mean square deviations again

Cluster analysis

Distance RMSD

Mutation 8

Brief check of the results

Visualization of the results

Quality assurance

Convergence of energy terms

Interaction Energy: Coulomb

Interaction Energy: Van der Waals

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

Ramachandran (phi/psi) plots=

Analysis of dynamics and time-averaged properties

Root mean square deviations again

Cluster analysis

Distance RMSD

References

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