Difference between revisions of "Molecular Dynamics Analysis GLA"

by Benjamin Drexler and Fabian Grandke

Introduction

In this task we analysed the simulated data that have been created within task 8. We used several tools of GROMACS to analyse the data and Pymol to visualize them.

Results

Brief check of the results

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

Wildtype Mutation 3 Mutation 8
2001 frames 2001 frames 2001 frames
time resolution of 5ps time resolution of 5ps time resolution of 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?

Wildtype Mutation 3 Mutation 8
18h06:37 18h29:13 18h19:11
13.252 ns/day 12.982 ns/day 13.101 ns/day
~206740 years ~211040 years ~209123 years

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

Wildtype Mutation 3 Mutation 8
-8.52573e+05 kJ/mol -8.53327e+05 kJ/mol -8.52539e+05 kJ/mol

Visualization of the results

Description Wildtype Mutation 3 Mutation 8
Plot
Molecular Dynamics simulation of the wildtype protein.
Molecular Dynamics simulation of the mutation 3 protein.
Molecular Dynamics simulation of the mutation 8 protein.

Quality assurance

Convergence of energy terms

Temperature

Description Wildtype Mutation 3 Mutation 8
Max(kJ/mol) 301.3734 302.0039 301.7407
Min(kJ/mol) 293.9565 294.0463 293.9268
Average(kJ/mol) 297.9275 297.9489 297.9303
Plot
Temperature over time for wildtype.
Temperature over time for mutation 3.
Temperature over time for mutation 8.

Pressure

Description Wildtype Mutation 3 Mutation 8
Max(kJ/mol) 346.2387 385.5467 326.9994
Min(kJ/mol) -308.7182 -357.4386 -291.1198
Average(kJ/mol) 0.4503482 -1.521002 -0.7279793
Plot
Pressure over time for wildtype.
Pressure over time for mutation 3.
Pressure over time for mutation 8.

Potential

Description Wildtype Mutation 3 Mutation 8
Max(kJ/mol) -849914.5 -850058.5 -849804.2
Min(kJ/mol) -855729.5 -856170.2 -855717.7
Average(kJ/mol) -852568.2 -853314.1 -852547.7
Plot
Potential over time for wildtype.
Potential over time for mutation 3.
Potential over time for mutation 8.

Total Energy

Description Wildtype Mutation 3 Mutation 8
Max(kJ/mol) -695814.5 -696662.8 -695560
Min(kJ/mol) -703550.4 -703769 -702829.8
Average(kJ/mol) -699602.2 -700202.2 -699497.3
Plot
Total energy over time for wildtype.
Total energy over time for mutation 3.
Total energy over time for mutation 8.

Minimum distances between periodic images

Description Wildtype Mutation 3 Mutation 8
Minimum distance(nm) 1.932 1.992 2.007
Time of occurance 370 7910 5940
Plot
Minimum distance between periodic boundary cells for wildtype.
Minimum distance between periodic boundary cells for mutation 3.
Minimum distance between periodic boundary cells for mutation 8.

Root mean square fluctuations

Description Wildtype Mutation 3 Mutation 8
Plot
Root mean square fluctuations for wildtype protein.
Root mean square fluctuations for mutation 3 protein.
Root mean square fluctuations for mutation 8 protein.
Plot
Root mean square fluctuations for wildtype C-alpha.
Root mean square fluctuations for mutation 3 C-alpha.
Root mean square fluctuations for mutation 8 C-alpha.

Description Wildtype Mutation 3 Mutation 8
Plot
Radius of gyration over time for wildtype protein.
Radius of gyration over time for mutation 3 protein.
Radius of gyration over time for mutation 8 protein.

Solvent accessible surface area

Description Wildtype Mutation 3 Mutation 8
Plot
Solvent accessible surface area over time for wildtype protein.
Solvent accessible surface area over time for mutation 3 protein.
Solvent accessible surface area over time for mutation 8 protein.
Plot
Solvent accessible surface area per atom for wildtype protein.
Solvent accessible surface area per atom for mutation 3 protein.
Solvent accessible surface area per atom for mutation 8 protein.
Plot
Solvent accessible surface area per residue for wildtype protein.
Solvent accessible surface area per residue for mutation 3 protein.
Solvent accessible surface area per residue for mutation 8 protein.

Hydrogen bonds

Description Wildtype Mutation 3 Mutation 8
Plot
Internal hydrogen bonds over time for wildtype protein.
Internal hydrogen bonds over time for mutation 3 protein.
Internal hydrogen bonds over time for mutation 8 protein.
Plot
Hydrogen bonds between protein and surrounding solvents for wildtype protein.
Hydrogen bonds between protein and surrounding solvents for mutation 3 protein.
Hydrogen bonds between protein and surrounding solvents for mutation 8 protein.

Ramachandran (phi/psi) plots

General Ramachandran Wildtype Mutation 3 Mutation 8
General ramachandran plot.<ref name=rama_wiki>http://en.wikipedia.org/wiki/Ramachandran_plot</ref>
Internal hydrogen bonds over time for wildtype protein.
Internal hydrogen bonds over time for mutation 3 protein.
Internal hydrogen bonds over time for mutation 8 protein.

Analysis of dynamics and time-averaged properties

Root mean square deviations again

Description Wildtype Mutation 3 Mutation 8
Plot
RMSD matrix for wildtype protein.
RMSD matrix for mutation 3 protein.
RMSD matrix for mutation 8 protein.

Cluster analysis

Description Wildtype Mutation 3 Mutation 8
Plot
RMS distribution for wildtype protein.
RMS distribution for mutation 3 protein.
RMS distribution for mutation 8 protein.

Distance RMSD

Description Wildtype Mutation 3 Mutation 8
Plot
RMS deviation for wildtype protein.
RMS deviation for mutation 3 protein.
RMS deviation for mutation 8 protein.

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