Molecular Dynamics Simulations Analysis of Glucocerebrosidase
From Bioinformatikpedia
Contents
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
Quality assurance
Convergence of energy terms
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
