Molecular Dynamics Analysis GLA
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by Benjamin Drexler and Fabian Grandke
Contents
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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