A brief check of results
To verified that the simulations finished properly we first use the command
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
|
Energy
|
Average
|
Err.Est.
|
RMSD
|
Tot-Drift (bar)
|
Pressure |
1.01601 |
0.015 |
71.2152 |
-0.0706383
|
|
Temperature
|
Energy
|
Average
|
Err.Est.
|
RMSD
|
Tot-Drift (K)
|
Temperature |
297.941 |
0.0047 |
0.954498 |
0.00557078
|
|
Potential
|
Energy
|
Average
|
Err.Est.
|
RMSD
|
Tot-Drift (kJ/mol)
|
Potential |
-1.24431e+06 |
66 |
1041.57 |
-463.992
|
|
Total Energy
|
Energy
|
Average
|
Err.Est.
|
RMSD
|
Tot-Drift (kJ/mol)
|
Total Energy |
-1.02119e+06 |
65 |
1279.76 |
-459.819
|
|
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
g_rmsf -f wtMD.xtc -s wtMD.tpr -o rmsf-per-residue.xvg -ox average.pdb -oq bfactors.pdb -res
RMSF for protein
RMSF for C-alpha