Molecular Dynamics Simulations Analysis (PKU)

Short Introduction

We will analyze our completed molecular dynamics simulations, following the task description and the tutorial of the Utrecht University Molecular Modeling Practical. We have completed one run for the wildtype protein and for the mutations ALA322GLY and ARG408TRP, a second run of the wildtype is pending. The second run for the wildtype might be necessary as the trajectory of the wildtype differs significantly from both the mutants. The commands used to generate plots, images etc. can be found in our journal.

Initial Checks

All three simulations run for the desired 10 ns, the trajectories contain 2000 frames in 5 ps steps each. The wildtype simulation took significantly longer, since we used only 16 cores for the widtype, 32 for the mutants. Almost half of the calculation time, 44.2% in each run, is spent on calculating Coulomb interactions and the Lennard-Jones potential of the solvent molecules. A few key statistics can be found in <xr id="tab:simulation_stats"/>.

<figtable id="tab:simulation_stats"> Statistics of the MD simulations

Mutation	Sim. time	Sim. speed	time to reach 1 s
Wildtype	11:32 h	20.8 ns/day	131,621 years
ALA322GLY	4:20 h	55.3 ns/day	49,543 years
ARG408TRP	4:26 h	54.1 ns/day	50,685 years

</figtable>

Wildtype analysis

Overlay of all frames of the 10 ns simulation of the wildtype phenylalanine hydroxylase structure 1J8U.

</figure>

Quality Assurance

Convergence of Energy Terms

Plot of the system temperature during the 10 ns simulation of the wildtype phenylalanine hydroxylase structure 1J8U. A running average in a window of length 100 ps is indicated in red.

</figure>

Plot of the system pressure during the 10 ns simulation of the wildtype phenylalanine hydroxylase structure 1J8U. A running average in a window of length 100 ps is indicated in red.

</figure>

Plot of the system volume during the 10 ns simulation of the wildtype phenylalanine hydroxylase structure 1J8U. A running average in a window of length 100 ps is indicated in red.

</figure>

Plot of the system density during the 10 ns simulation of the wildtype phenylalanine hydroxylase structure 1J8U. A running average in a window of length 100 ps is indicated in red.

</figure>

Plot of the system extension in 3 dimensions during the 10 ns simulation of the wildtype phenylalanine hydroxylase structure 1J8U.

box

</figure>

What is the average temperature and what is the heat capacity of the system? ( T )
What are the terms plotted in the files energy.xvg and box.xvg
Estimate the plateau values for the pressure, the volume and the density. ( T )
What are the terms plotted in the files coulomb-inter.xvg and vanderwaals-inter.xvg ?

Minimum Distance Between Periodic Images

What was the minimal distance between periodic images and at what time did that occur?
What happens if the minimal distance becomes shorter than the cut-off distance used for electrostatic interactions? Is it the case in your simulations? (It also matters if the small distance occurs transiently or if it is persistent. If it is persistent, it is likely affecting the protein dynamics; but if it's just transiently than it will hardly, if at all, influence.)
Run now g_mindist on the C-alpha group, does it change the results? What does is mean for your system? (Ideally, the minimal distance should therefore not be less than two nanometers.)

Root Mean Square Fluctuations

Indicate the start and end residue for the most flexible regions and the maximum amplitudes. ( T )
Compare the results from the different proteins. Are there differences? If yes, which is the most flexible and which least?

Convergence of RMSD

If observed, at what time and value does the RMSD reach a plateau?
Briefly discuss differences between the graphs against the starting structure and against the average structure. Which is a better measure for convergence?

Convergence of Radius of Gyration

Have a look at the radius of gyration and the individual components and note how each of these progress to an equilibrium value.
At what time and value does the radius of gyration converge? ( T )

Structural Analysis: Properties Derived from Configurations

Solvent accessible surface

Which residues are the most accessible to the solvent?

Hydrogen Bonds

Discuss the relation between the number of hydrogen bonds for both cases and the fluctuations in each plot.

Salt Bridges

Secondary Structure

Discuss some of the changes in the secondary structure, if any.

Ramachandran Plots

What can you say about the conformation of the residues, based on the ramachandran plots?

Aanalysis of Dynamics and Time-averaged Properties

Root Mean Square Deviations

What is interesting by choosing the group "Mainchain+Cb" for this analysis?
How many transitions do you see?
What can you conclude from this analysis? Could you expect such a result, justify?

Cluster Analysis

How many clusters were found and what were the sizes of the largest two?
Are there notable differences between the two structures?

Distance RMSD

At what time and value does the dRMSD converge and how does this graph compare to the standard RMSD?