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

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.

Convergence of radius of gyration

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.

References

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