Molecular Dynamics Analysis GLA

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Revision as of 23:08, 8 October 2011 by Grandke (talk | contribs)

by Benjamin Drexler and Fabian Grandke


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.




Brief check of the results

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

Wildtype Mutation 3 Mutation 8
2001 frames 2001 frames 2001 frames
time resolution of 5ps time resolution of 5ps time resolution of 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?

Wildtype Mutation 3 Mutation 8
18h06:37 18h29:13 18h19:11
13.252 ns/day 12.982 ns/day 13.101 ns/day
~206740 years ~211040 years ~209123 years

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

Wildtype Mutation 3 Mutation 8
-8.52573e+05 kJ/mol -8.53327e+05 kJ/mol -8.52539e+05 kJ/mol

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


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