Task 10: Molecular Dynamics Analysis
A BRIEF CHECK OF RESULTS
In order to verify that our simulation ran successfully we used the command line tool gmxcheck. we executed it as follows for our .xtc file:
gmxcheck -f 1J8U_nosol_after_SCWRL_no_h_merged_crystal_water_md.xtc
How many frames are in the trajectory file and what is the time resolution?
We observed 2001 frames with a 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?
The simulation ran 4h00:39 and had a simulation speed of 59.835 ns/day. To calculate 1 second we would need (1 / (59 * (10^(-9)))) / 365 = 46 436.0344 years
Which contribution to the potential energy accounts for most of the calculations?
- potential energy: -4.57312e+05 kJ/mol
VISUALIZATION OF RESULTS
We extracted 1000 frames from the trajectory (-dt 10), leaving out the water (selected Protein when asked for a selection). Moreover, we will remove the jumps over the boundaries and make a continuous trajectory (-pbc nojump):
trjconv -s 1J8U_nosol_after_SCWRL_no_h_merged_crystal_water_md.tpr -f 1J8U_nosol_after_SCWRL_no_h_merged_crystal_water_md.xtc -o protein.pdb -pbc nojump -dt 10