Canavan Task 10 - Molecular Dynamics Simulations

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Revision as of 17:23, 28 July 2012 by Vorbergs (talk | contribs) (Potential Energy)


Further information and commands can be found in the protocol.

Initial Checks

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.

<figtable id="gmxcheck">

<xr nolink id="gmxcheck"/> Results from gmxcheck and the logfile
WT K213E A305E
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.


<figtable id="energies_temp">

<xr nolink id="energies_temp"/> Quality check for convergence of energy values: temperature.
WT K213E A305E
Reference Value 298 K 298 K 298 K
Average 297.914 K 297.908 297.917
Err.Est. 0.0072 0.0059 0.0047
RMSD 1.38693 1.38991 1.3981
Total Drift -0.00042403 (K) 0.00867898 (K) 0.0154339 (K)
Plot <figure id="wt_temp">
<xr nolink id="wt_temp"/>
<figure id="a305_scwrl_temp.png">
<xr nolink id="a305_scwrl_temp.png"/>
Temperature of the system for A305E smoothed over a window of 20.



<figtable id="energies_temp">

<xr nolink id="energies_temp"/> Quality check for convergence of energy values: pressure.
WT K213E A305E
Reference Value 1.0 (Berendsen barostat) 1.0 (Berendsen barostat) 1.0 (Berendsen barostat)
Average 1.00763 1.00683 1.00797
Err.Est. 0.018 0.015 0.022
RMSD 111.943 112.761 112.987
Total Drift -0.0713928 (bar) -0.0585283 (bar) -0.100316 (bar)
Plot <figure id="wt_pressure">
<xr nolink id="wt_pressure"/>


Potential Energy

<figtable id="energies_potential">

<xr nolink id="energies_potential"/> Quality check for convergence of energy values: potential energy.
WT K213E A305E
Average -592161 -585993 -583187
Err.Est. 55 65 46
RMSD 721.947 726.81 722.076
Total Drift -252.112 (kJ/mol) -425.823 (kJ/mol) -290.165 (kJ/mol)
Plot <figure id="wt_potential">
<xr nolink id="wt_potential"/>
><figure id="a305_scwrl_potenergy">
<xr nolink id="a305_scwrl_potenergy"/>


Total energy

<figtable id="energies_total">

<xr nolink id="energies_total"/> Quality check for convergence of energy values: total energy.
WT K213E A305E
Average -485680 -480905 -478506
Err.Est. 54 64 45
RMSD 886.726 888.522 887.724
Total Drift -252.262 (kJ/mol) -422.763 (kJ/mol) -284.743 (kJ/mol)
Plot <figure id="wt_tot_energy">
<xr nolink id="wt_tot_energy"/>
<figure id="a305e_scwrl_totenergy">
<xr nolink id="a305e_scwrl_totenergy"/>
Total energy of the system for A305E smoothed over a window of 20


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.

<figtable id="wt_pi">

<figure id="wt_pi_ca">
<xr nolink id="wt_pi_ca"/>
<figure id="wt_pi">
<xr nolink 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.

<figtable id="wt_rmsf">

<figure id="wt_rmsf_plot">
<xr nolink id="wt_rmsf_plot"/>
<figure id="wt_bfactors">
<xr nolink id="wt_bfactors"/>
<figure id="wt_average">
<xr nolink 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.

<figtable id="CD_wt_rmsf">

<figure id="wt_rmsd_all_vs_first">
<xr nolink id="wt_rmsd_all_vs_first"/>
<figure id="wt_rmsd_all_vs_average">
<xr nolink id="wt_rmsd_all_vs_average"/>
<figure id="wt_rmsd_calpha_vs_first">
<xr nolink id="wt_rmsd_calpha_vs_first"/>
<figure id="wt_rmsd_calpha_vs_average">
<xr nolink 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.

<figure id="wt_rg">

<xr nolink id="wt_rg"/>