Molecular Dynamics Analysis BCKDHA
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
- 4 Structural analysis
- 5 Analysis of dynamics and time-averaged properties
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
Pressure
|
Temperature
|
Potential
|
Total Energy
|
Minimum distance between periodic boundary cells
To calculate the minimum distance we used the command
g_mindist -f wtMD.xtc -s wtMD.tpr -od minimal-periodic-distance.xvg -pi
After submitting this command we chose group 1 to calculate the minimum distance for the whole protein.
Shortest periodic distance is 1.40945 (nm) at time 6090 (ps) between atoms 25 and 6490.
Root mean square fluctuations
To calculate the minimum distance we used the command
g_rmsf -f wtMD.xtc -s wtMD.tpr -o rmsf-per-residue.xvg -ox average.pdb -oq bfactors.pdb -res
After submitting this command we had to choose the group we want the RMSF to be calculated for:
- Protein: 1
- C-alpha: 3
RMSF for protein
RMSF for C-alpha
Pymol analysis of average and bfactor
To analyze the average and the bfactor we used pymol.
Protein
1u5b/bfactors | 1u5b/average | bfactors/average |
---|---|---|
RMSD: 0.377 | RMSD: 1.169 | RMSD: 1.422 |
C-alpha
1u5b/bfactors | 1u5b/average | bfactors/average |
---|---|---|
RMSD: 0.300 | RMSD: 0.955 | RMSD: 0.993 |
Radius of gyration
To calculate the radius of gyration we used the command
g_gyrate -f wtMD.xtc -s wtMD.tpr -o radius-of-gyration.xvg
After submitting this command we chose group 1 to calculate the radius of gyration for the whole protein
Structural analysis
First we had to use the command
trjconv -f wtMD.xtc -o wtMD_nojump.xtc -pbc nojump
This is important because the protein possibly jumpes out of the box so the trajectory has to be rebuild. This has the effect that the particles are back in the center.
Solvent accessible surface area
To calculate the solvent accessible surface area we used the command
g_sas -f wtMD_nojump.xtc -s wtMD.tpr -o solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg
After submitting this command we had to choose two groups. Both times we chose protein.
Solvent accessible surface | SAS over time per residue | SAS over time per atom |
---|---|---|
Hydrogen bonds
To calculate the hydrogen bonds between protein and protein and between protein and water we used the commands
echo 1 1 | g_hbond -f wtMD_nojump.xtc -s wtMD.tpr -num hydrogen-bonds-intra-protein.xvg
echo 1 12 | g_hbond -f wtMD_nojump.xtc -s wtMD.tpr -num hydrogen-bonds-protein-water.xvg
protein and protein | protein and water |
---|---|
salt bridges
Ramachandran plot
To calculate the ramachandran plot we used the command
g_rama -f wtMD_nojump.xtc -s wtMD.tpr -o ramachandran.xvg
Analysis of dynamics and time-averaged properties
RMSD matrix
To calculate the RMSD matrix we used the command
g_rms -s wtMD.tpr -f wtMD_nojump.xtc -f2 wtMD_nojump.xtc -m rmsd-matrix.xpm -dt 10
After submitting this command we had to choose two groups. Both times we chose protein.
cluster analysis
To calculate the cluster we used the command
echo 6 6 | g_cluster -s wtMD.tpr -f wtMD_nojump.xtc -dm rmsd-matrix.xpm -dist rmsd-distribution.xvg -o clusters.xpm -sz cluster-sizes.xvg -tr cluster-transitions.xpm -ntr cluster-transitions.xvg -clid cluster-id-over-time.xvg -cl clusters.pdb -cutoff 0.1 -method gromos -dt 10