A brief check of results
We briefly checked the length of the MD simulations via gmxcheck:
gmxcheck -f traj.xtc
Since we used the AGroS paramter -lengthMD 10, we expected the MD simulation to be 10ns long. gmxcheck reported for each simulation 2001 frames and a time step of 5ps per frame which amounts to the expected length of 2001*5ps=10ns.
We further investigated the runtime of the MD simulation by looking at the log files. The simulation of the WT took approximately twice as long as the other two mutations since we used only 16 instead of 32 cores. Performing a MD simulation over 1s would take more than 100000 years if the same hardware were used than we did.
<figtable id="tab:runtime">
| Name |
Runtime |
ns/day |
years/1s
|
|
|
| WT |
16h25:59 |
14.605 |
187536
|
| L470P |
9h20:49 |
25.677 |
106699
|
| W209R |
9h18:47 |
25.770 |
106314
|
Runtime of the MD simulations and the estimated runtime for a simulation length of 1s.
</figtable>
The computation of the energy term Coul(T) + LJ [W3-W3] accounted for most (47%) of the floating point operations.
Visualization
</figure>
</figure>
</figure>
| <figure id="fig:gif_wt"> |
Wildtype
| <figure id="fig:gif_L470P"> |
L470P
| <figure id="fig:gif_W209R"> |
W209RVisualization of the MD simulations. Red: the active site residues E235 and E340; Blue: the mutated residue.
Quality assurance
</figure>
</figure>
</figure>
| <figure id="fig:qual_pres_wt"> |
Wildtype (1.0069/-0.0423231)
| <figure id="fig:qual_pres_L470P"> |
L470P (0.996977/0.0144563)
| <figure id="fig:qual_pres_W209R"> |
W209R (1.00887/0.00535799)Development of the pressure during the MD simulation. In bracket: average/total-drift.
</figure>
</figure>
</figure>
| <figure id="fig:qual_temp_wt"> |
Wildtype (297.912/0.00443415)
| <figure id="fig:qual_temp_L470P"> |
L470P (297.907/-0.00147577)
| <figure id="fig:qual_temp_W209R"> |
W209R (297.915/0.0095005)Development of the temperature during the MD simulation. In bracket: average/total-drift.
</figure>
</figure>
</figure>
| <figure id="fig:qual_pot_wt"> |
Wildtype (-939801/-450.018)
| <figure id="fig:qual_pot_L470P"> |
L470P (-940007/-705.14)
| <figure id="fig:qual_pot_W209R"> |
W209R (-940568/-355.406)Development of the potential energy during the MD simulation. In bracket: average/total-drift.
</figure>
</figure>
</figure>
| <figure id="fig:qual_tot_wt"> |
Wildtype (-768901/-447.47)
| <figure id="fig:qual_tot_L470P"> |
L470P (-769094/-705.985)
| <figure id="fig:qual_tot_W209R"> |
W209R (-769675/-349.952)Development of the total energy during the MD simulation. In bracket: average/total-drift.
