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

Mutation 7

still waiting

Mutation 10

still waiting