Canavan Task 10 - Molecular Dynamics Simulations
Further information and commands can be found in the protocol.
For all three runs, there are 2000 time frames, with a resolution of 5 psec. Therefore the whole simulation ran for 10000 psec = 10 nsec.
|run time||5h 22:37||5h 08:54||5h 08:35|
|atoms outside of box||406, 408, 480, 482, 483, 484, 485, 486, 500, 501,..||406, 480, 482, 483, 484, 485, 486, 500, 502, 503,..||406, 408, 480, 482, 483, 484, 485, 486, 500, 501,..|
|Last frame||2000 time 10000.000||2000 time 10000.000||2000 time 10000.000|
For all analysed thermodynamical parameters convergence could be observed. Though, for pressure the values vary enormously, but the average pressure is close to the specified value of 1 bar.
|Reference Value||298 K||298 K||298 K|
|Total Drift||-0.00042403 (K)||0.00867898 (K)||0.0154339 (K)|
|Plot||<figure id="wt_temp">||<figure id="a305_scwrl_temp.png">|
|Reference Value||1.0 (Berendsen barostat)||1.0 (Berendsen barostat)||1.0 (Berendsen barostat)|
|Total Drift||-0.0713928 (bar)||-0.0585283 (bar)||-0.100316 (bar)|
|Total Drift||-252.112 (kJ/mol)||-425.823 (kJ/mol)||-290.165 (kJ/mol)|
|Plot||<figure id="CD_wt_potenergy">||<figure id="a305_scwrl_potenergy">|
|Total Drift||-252.262 (kJ/mol)||-422.763 (kJ/mol)||-284.743 (kJ/mol)|
|Plot||<figure id="wt_tot_energy">||<figure id="a305e_scwrl_totenergy">|
distances between periodic boundaries
The shortest periodic distance is 1.6456 (nm) at time 7675 (ps), between atoms 15 and 4507.
As expected the minimum distance to periodic images is larger when only considering C-alpha atoms, than for the whole protein with all sidechains. The suggested distance limit of 2nm is undercut for at some timesteps during the simulation.
|<figure id="wt_pi_ca">||<figure id="wt_pi">|
Only small fluctuations can be observed for the residues of the wildtype protein. There is a region between residues 120 and 180 that is especially rigid.
When looking at the bfactors one finds the same results. The whole protein is rather rigid and only some exposed loops have higher bfactors.
For exposed residues the averaged structure shows several possible residue conformers.
|<figure id="wt_rmsf_plot">||<figure id="wt_bfactors">||<figure id="wt_average">|
Convergence of RMSD
As expected, the RMSD increases when using the starting structure as a reference. Over the simulation the structure changes and deviates more and more from the starting structure. Yet these changes are not tremendous, as the starting structure is the crystal structure and therefore should already have adopted a optimal conformation.
When taking the average structure as reference, the RMSD is higher at the beginning of the simulation and finally converges as the structure reaches an equilibrium.
When only taking the Calpha atoms into accounts, the deviations are even smaller, than when also calculating RMSD values for the flexible side chains.
|<figure id="wt_rmsd_all_vs_first">||<figure id="wt_rmsd_all_vs_average">||<figure id="wt_rmsd_calpha_vs_first">||<figure id="wt_rmsd_calpha_vs_average">|
Radius of gyration
Against our expectations, the radius of gyration increases for the wildtype protein. As the energy of the system decreases during hte rund, we would expect that the protein becomes more compact. One idea is, that we used the monomeric form of the protein for the simulation, whereas in the crystal structure it is a dimer.