Molecular Dynamics Simulations Analysis of Glucocerebrosidase

Introduction

To analyze our Molecular Dynamics Simulations we followed the tutorial described here: http://md.chem.rug.nl/~mdcourse/analysis1.html

Wildtype

A brief check of results

• command: gmxcheck -f 2NT0_wt_md.xtc

How many frames are in the trajectory file and what is the time resolution?

• 2001 frames
• timestep: 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?

• Simulation run: 8h37:36
• Simulation speed: 27.821
• Time to reach a second: 1/0.000000028 = 35714285,714285714 days = 97847,358121331 years

Which contribution to the potential energy accounts for most of the calculations?

• -9.39801e+05 kJ/mol

Visualization of results

For visualization we extract 1000 frames from the trajectory (-dt 10), only select the protein without the water and remove the jumps over the boundaries to make a continuous trajectory (-pbc nojump).

• command: trjconv -s 2NT0_wt_md.tpr -f 2NT0_wt_md.xtc -o protein.pdb -pbc nojump -dt 10

Figure 1: The protein with the spectrum

Figure 2: The protein with the box around it

Figure 3: The cartoon presentation after using the command dss

Figure 4: The active site

STILL MISSING: movie

Quality assurance

Convergence of energy terms

First we look at the energy terms. Therefore we look at the temperature, the pressure, the energy, the volume, the density, the box and the interaction energies between protein and solvent (Coulomb and van der Waals).

With the following commands we produced *.xvg files which were visualized with xmgrace.

g_energy -f 2NT0_wt_md.edr -o temperature.xvg
g_energy -f 2NT0_wt_md.edr -o pressure.xvg
g_energy -f 2NT0_wt_md.edr -o energy.xvg
g_energy -f 2NT0_wt_md.edr -o volume.xvg
g_energy -f 2NT0_wt_md.edr -o density.xvg
g_energy -f 2NT0_wt_md.edr -o box.xvg

Temperature

Figure 6: Temperature of the Molecular Dynamics Simulation of the Wildtype

Energy	Average	Err.Est.	RMSD	Tot-Drift
Temperature	297.912	0.0062	1.08924	0.00616934 (K)

What is the average temperature and what is the heat capacity of the system?
297.912 K

In figure 6 you can see the plot for the temperature during the simulation. It fluctuates between 295 K and 301 K. So the temperature is very stable, the difference is only six Kelvin. That means that the system reached very soon a stable temperature.

Pressure

Figure 7: Pressure of the Molecular Dynamics Simulation of the Wildtype

Energy	Average	Err.Est.	RMSD	Tot-Drift
Pressure	1.00032	0.014	87.9016	0.0583997 (bar)

Estimate the plateau values for the pressure.
0 bar? 1.00032 bar? higher?

The pressure fluctuates around -300 bar and +300 bar. That is a difference of 600 bar which is very large. The system seems not to have reached its plateau. So it is also hard to estimate such a value because no trend is observable.

Energy

Figure 8: Energies of the Molecular Dynamics Simulation of the Wildtype

Energy	Average	Err.Est.	RMSD	Tot-Drift
Potential	-939801	85	924.013	-583.172 (kJ/mol)
Kinetic En.	170900	3.6	624.851	3.53909 (kJ/mol)
Total Energy	-768901	84	1128.21	-579.63 (kJ/mol)

What are the terms plotted in the file energy.xvg?
potential, kinetic and total energy

In the plot you can see that all three energy terms reached a plateau. It is hard to say how large the fluctuations are, because the scale is too large. But as they converged the simulation seems to have reached its optimum.

Volume

Figure 9: Volume of the Molecular Dynamics Simulation of the Wildtype

Energy	Average	Err.Est.	RMSD	Tot-Drift
Volume	735.655	0.042	0.552925	-0.0802412 (nm^3)

Estimate the plateau values for the volume.
735.655? 736?

In figure 9 you can see the volume fluctuating between 734 nm³ and 737 nm³. The difference is only three nm³. So the colume also converged to a an interval.

Density

Figure 10: Density of the Molecular Dynamics Simulation of the Wildtype

Energy	Average	Err.Est.	RMSD	Tot-Drift
Density	1009.64	0.058	0.75885	0.110104 (kg/m^3)

Estimate the plateau values for the density.
1009.64? 1010?

In figure 10 you can see the density fluctuating around 1010 kg/m³. The difference seems to be about 5 kg/m³. So the density also converged.

Box

Figure 11: Boxes of the Molecular Dynamics Simulation of the Wildtype

Energy	Average	Err.Est.	RMSD	Tot-Drift
Box-X	10.1328	0.0002	0.00253864	-0.000368389 (nm)
Box-Y	10.1328	0.0002	0.00253864	-0.000368389 (nm)
Box-Z	7.16498	0.00014	0.00179508	-0.000260487 (nm)

What are the terms plotted in the file box.xvg?
The size of the box around the protein.

In figure 11 you can see the sizes of the box, the x-, the y- and the z-term. They are very constant with 10.1328, 10.1328 and 7.16498 nm.

Interaction Energy: Coulomb

Figure 12: Interaction energy of protein and solvent

Energy	Average	Err.Est.	RMSD	Tot-Drift
Coul-SR:Protein-non-Protein	-24690.5	120	476.146	-405.451 (kJ/mol)
Coul-14:Protein-non-Protein	0	0	0	0 (kJ/mol)

In figure 12 you can see the Coulomb Energy. It has its average at -24690.5 kJ/mol. It fluctuates around that value in an interval of about 1000 kJ/mol. At the end it is more stable. As the equilibration takes longer for this term it may be that the value at the time 8000 to 10000 is the equilibrium.

Interaction Energy: van der Waals

Figure 13: Interaction energy of protein and solvent

Energy	Average	Err.Est.	RMSD	Tot-Drift
LJ-SR:Protein-non-Protein	-3184.89	4.3	149.546	-12.8142 (kJ/mol)
LJ-14:Protein-non-Protein	0	0	0	0 (kJ/mol)

In figure 13 you can see the van der Waals interaction energy. It has its average at -3184.89. The values are fluctuating in an interval of about 1000 kJ/mol. Also at the end of the time there is no equilibration recognisable. Maybe it always fluctuates in such a big interval or it needs more time to converge.

Minimum distances between periodic images

Figure 14: Minima periodic distance on the protein

What was the minimal distance between periodic images and at what time did that occur?

The shortest periodic distance is 1.97143 (nm) at time 5825 (ps), between atoms 960 and 2323.

Figure 14: Minima periodic distance on the C-alpha group

What was the minimal distance between periodic images and at what time did that occur?

The shortest periodic distance is 2.43551 (nm) at time 5345 (ps), between atoms 952 and 2267.

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 is not the case in our simulation. The energy would "explode".

Run now g_mindist on the C-alpha group, does it change the results? What does is mean for your system?

It changes to a greater distance between two other atoms (952 and 2267). That means that it may be atoms of a side group that have this minimal distance. Also the fluctuation interval of the minimum distance becomes smaller.

Mutation 7

still waiting

Mutation 10

still waiting