Molecular Dynamics Analysis BCKDHA
From Bioinformatikpedia
Contents
- 1 A brief check of results
- 1.1 How many frames are in the trajectory file and what is the time resolution?
- 1.2 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?
- 1.3 Which contribution to the potential energy accounts for most of the calculations?
- 2 Visualization of results
- 3 Quality assurance
A brief check of results
To verified that the simulations finished properly we first use the command
gmxcheck -f wt.xtc
How many frames are in the trajectory file and what is the time resolution?
- frames: 2001
- time resolution: 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?
- real time: 9h27:35
- simulation speed: 25.370 ns/day
- simulation speed: 107991 years/second
Which contribution to the potential energy accounts for most of the calculations?
- potential energy: -1.24431e+06
Visualization of results
To get a pdb file to be able to visualize the model with pymol we used the Swiss army knife gromacs tool trjconv:
trjconv -s wt.tpr -f wt.xtc -o protein.pdb -pbc nojump -dt 10
Quality assurance
Energy calculations
To calculate the different energies we used the command:
g_energy -f wtMD.edr -o energy.xvg
After submitting this command we had to choose the energy which should calculated.
- Pressure: 13
- Temperature: 12
- Potential: 9
- Total Energy: 11