Difference between revisions of "Molecular Dynamics Analysis GLA"
From Bioinformatikpedia
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− | | [[Image:GLA_Wt_animation.gif|thumb|100px|Molecular Dynamics simulation of the wildtype protein.]] |
+ | | [[Image:GLA_Wt_animation.gif|thumb|100px|Figure 1: Molecular Dynamics simulation of the wildtype protein.]] |
− | | [[Image:GLA_3_animation.gif|thumb|100px|Molecular Dynamics simulation of the mutation 3 protein.]] |
+ | | [[Image:GLA_3_animation.gif|thumb|100px|Figure 2: Molecular Dynamics simulation of the mutation 3 protein.]] |
− | | [[Image:GLA_8_animation.gif|thumb|100px|Molecular Dynamics simulation of the mutation 8 protein.]] |
+ | | [[Image:GLA_8_animation.gif|thumb|100px|Figure 3: Molecular Dynamics simulation of the mutation 8 protein.]] |
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− | | [[Image:GLA_Wt_temp.png|thumb|100px|Temperature over time for wildtype.]] |
+ | | [[Image:GLA_Wt_temp.png|thumb|100px|Figure 4: Temperature over time for wildtype.]] |
− | | [[Image:GLA_3_temp.png|thumb|100px|Temperature over time for mutation 3.]] |
+ | | [[Image:GLA_3_temp.png|thumb|100px|Figure 5: Temperature over time for mutation 3.]] |
− | | [[Image:GLA_8_temp.png|thumb|100px|Temperature over time for mutation 8.]] |
+ | | [[Image:GLA_8_temp.png|thumb|100px|Figure 6: Temperature over time for mutation 8.]] |
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− | | [[Image:GLA_Wt_pressure.png|thumb|100px|Pressure over time for wildtype.]] |
+ | | [[Image:GLA_Wt_pressure.png|thumb|100px|Figure 7: Pressure over time for wildtype.]] |
− | | [[Image:GLA_3_pressure.png|thumb|100px|Pressure over time for mutation 3.]] |
+ | | [[Image:GLA_3_pressure.png|thumb|100px|Figure 8: Pressure over time for mutation 3.]] |
− | | [[Image:GLA_8_pressure.png|thumb|100px|Pressure over time for mutation 8.]] |
+ | | [[Image:GLA_8_pressure.png|thumb|100px|Figure 9: Pressure over time for mutation 8.]] |
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− | | [[Image:GLA_Wt_potent.png|thumb|100px|Potential over time for wildtype.]] |
+ | | [[Image:GLA_Wt_potent.png|thumb|100px|Figure 10: Potential over time for wildtype.]] |
− | | [[Image:GLA_3_potent.png|thumb|100px|Potential over time for mutation 3.]] |
+ | | [[Image:GLA_3_potent.png|thumb|100px|Figure 11: Potential over time for mutation 3.]] |
− | | [[Image:GLA_8_potent.png|thumb|100px|Potential over time for mutation 8.]] |
+ | | [[Image:GLA_8_potent.png|thumb|100px|Figure 12: Potential over time for mutation 8.]] |
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− | | [[Image:GLA_Wt_ener.png|thumb|100px|Total energy over time for wildtype.]] |
+ | | [[Image:GLA_Wt_ener.png|thumb|100px|Figure 13: Total energy over time for wildtype.]] |
− | | [[Image:GLA_3_ener.png|thumb|100px|Total energy over time for mutation 3.]] |
+ | | [[Image:GLA_3_ener.png|thumb|100px|Figure 14: Total energy over time for mutation 3.]] |
− | | [[Image:GLA_8_ener.png|thumb|100px|Total energy over time for mutation 8.]] |
+ | | [[Image:GLA_8_ener.png|thumb|100px|Figure 15: Total energy over time for mutation 8.]] |
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− | | [[Image:GLA_Wt_mindist.png|thumb|100px|Minimum distance between periodic boundary cells for wildtype.]] |
+ | | [[Image:GLA_Wt_mindist.png|thumb|100px|Figure 16: Minimum distance between periodic boundary cells for wildtype.]] |
− | | [[Image:GLA_3_mindist.png|thumb|100px|Minimum distance between periodic boundary cells for mutation 3.]] |
+ | | [[Image:GLA_3_mindist.png|thumb|100px|Figure 17: Minimum distance between periodic boundary cells for mutation 3.]] |
− | | [[Image:GLA_8_mindist.png|thumb|100px|Minimum distance between periodic boundary cells for mutation 8.]] |
+ | | [[Image:GLA_8_mindist.png|thumb|100px|Figure 18: Minimum distance between periodic boundary cells for mutation 8.]] |
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− | | [[Image:GLA_Wt_rmsf.png|thumb|100px|Root mean square fluctuations for wildtype protein.]] |
+ | | [[Image:GLA_Wt_rmsf.png|thumb|100px|Figure 19: Root mean square fluctuations for wildtype protein.]] |
− | | [[Image:GLA_3_rmsf.png|thumb|100px|Root mean square fluctuations for mutation 3 protein.]] |
+ | | [[Image:GLA_3_rmsf.png|thumb|100px|Figure 20: Root mean square fluctuations for mutation 3 protein.]] |
− | | [[Image:GLA_8_rmsf.png|thumb|100px|Root mean square fluctuations for mutation 8 protein.]] |
+ | | [[Image:GLA_8_rmsf.png|thumb|100px|Figure 21: Root mean square fluctuations for mutation 8 protein.]] |
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− | | [[Image:GLA_Wt_rmsfc.png|thumb|100px|Root mean square fluctuations for wildtype C-alpha.]] |
+ | | [[Image:GLA_Wt_rmsfc.png|thumb|100px|Figure 22: Root mean square fluctuations for wildtype C-alpha.]] |
− | | [[Image:GLA_3_rmsfc.png|thumb|100px|Root mean square fluctuations for mutation 3 C-alpha.]] |
+ | | [[Image:GLA_3_rmsfc.png|thumb|100px|Figure 23: Root mean square fluctuations for mutation 3 C-alpha.]] |
− | | [[Image:GLA_8_rmsfc.png|thumb|100px|Root mean square fluctuations for mutation 8 C-alpha.]] |
+ | | [[Image:GLA_8_rmsfc.png|thumb|100px|Figure 24: Root mean square fluctuations for mutation 8 C-alpha.]] |
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− | | [[Image:GLA_Wt_avb.png|thumb|100px|Image of aligned average and b-factor protein for wildtype protein.]] |
+ | | [[Image:GLA_Wt_avb.png|thumb|100px|Figure 25: Image of aligned average and b-factor protein for wildtype protein.]] |
− | | [[Image:GLA_3_avb.png|thumb|100px|Image of aligned average and b-factor protein for mutation 3 protein.]] |
+ | | [[Image:GLA_3_avb.png|thumb|100px|Figure 26: Image of aligned average and b-factor protein for mutation 3 protein.]] |
− | | [[Image:GLA_8_avb.png|thumb|100px|Image of aligned average and b-factor protein for mutation 8 protein.]] |
+ | | [[Image:GLA_8_avb.png|thumb|100px|Figure 27: Image of aligned average and b-factor protein for mutation 8 protein.]] |
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− | | [[Image:GLA_Wt_avbc.png|thumb|100px|Image of aligned average and b-factor protein for wildtype C-alpha.]] |
+ | | [[Image:GLA_Wt_avbc.png|thumb|100px|Figure 28: Image of aligned average and b-factor protein for wildtype C-alpha.]] |
− | | [[Image:GLA_3_avbc.png|thumb|100px|Image of aligned average and b-factor protein for mutation 3 C-alpha.]] |
+ | | [[Image:GLA_3_avbc.png|thumb|100px|Figure 29: Image of aligned average and b-factor protein for mutation 3 C-alpha.]] |
− | | [[Image:GLA_8_avbc.png|thumb|100px|Image of aligned average and b-factor protein for mutation 8 C-alpha.]] |
+ | | [[Image:GLA_8_avbc.png|thumb|100px|Figure 30: Image of aligned average and b-factor protein for mutation 8 C-alpha.]] |
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− | | [[Image:GLA_Wt_radius.png|thumb|100px|Radius of gyration over time for wildtype protein.]] |
+ | | [[Image:GLA_Wt_radius.png|thumb|100px|Figure 31: Radius of gyration over time for wildtype protein.]] |
− | | [[Image:GLA_3_radius.png|thumb|100px|Radius of gyration over time for mutation 3 protein.]] |
+ | | [[Image:GLA_3_radius.png|thumb|100px|Figure 32: Radius of gyration over time for mutation 3 protein.]] |
− | | [[Image:GLA_8_radius.png|thumb|100px|Radius of gyration over time for mutation 8 protein.]] |
+ | | [[Image:GLA_8_radius.png|thumb|100px|Figure 33: Radius of gyration over time for mutation 8 protein.]] |
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− | | [[Image:GLA_Wt_sas.png|thumb|100px|Solvent accessible surface area over time for wildtype protein.]] |
+ | | [[Image:GLA_Wt_sas.png|thumb|100px|Figure 34: Solvent accessible surface area over time for wildtype protein.]] |
− | | [[Image:GLA_3_sas.png|thumb|100px|Solvent accessible surface area over time for mutation 3 protein.]] |
+ | | [[Image:GLA_3_sas.png|thumb|100px|Figure 35: Solvent accessible surface area over time for mutation 3 protein.]] |
− | | [[Image:GLA_8_sas.png|thumb|100px|Solvent accessible surface area over time for mutation 8 protein.]] |
+ | | [[Image:GLA_8_sas.png|thumb|100px|Figure 36: Solvent accessible surface area over time for mutation 8 protein.]] |
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− | | [[Image:GLA_Wt_sasa.png|thumb|100px|Solvent accessible surface area per atom for wildtype protein.]] |
+ | | [[Image:GLA_Wt_sasa.png|thumb|100px|Figure 37: Solvent accessible surface area per atom for wildtype protein.]] |
− | | [[Image:GLA_3_sasa.png|thumb|100px|Solvent accessible surface area per atom for mutation 3 protein.]] |
+ | | [[Image:GLA_3_sasa.png|thumb|100px|Figure 38: Solvent accessible surface area per atom for mutation 3 protein.]] |
− | | [[Image:GLA_8_sasa.png|thumb|100px|Solvent accessible surface area per atom for mutation 8 protein.]] |
+ | | [[Image:GLA_8_sasa.png|thumb|100px|Figure 39: Solvent accessible surface area per atom for mutation 8 protein.]] |
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− | | [[Image:GLA_Wt_sasr.png|thumb|100px|Solvent accessible surface area per residue for wildtype protein.]] |
+ | | [[Image:GLA_Wt_sasr.png|thumb|100px|Figure 40: Solvent accessible surface area per residue for wildtype protein.]] |
− | | [[Image:GLA_3_sasr.png|thumb|100px|Solvent accessible surface area per residue for mutation 3 protein.]] |
+ | | [[Image:GLA_3_sasr.png|thumb|100px|Figure 41: Solvent accessible surface area per residue for mutation 3 protein.]] |
− | | [[Image:GLA_8_sasr.png|thumb|100px|Solvent accessible surface area per residue for mutation 8 protein.]] |
+ | | [[Image:GLA_8_sasr.png|thumb|100px|Figure 42: Solvent accessible surface area per residue for mutation 8 protein.]] |
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− | | [[Image:GLA_Wt_hbip.png|thumb|100px|Internal hydrogen bonds over time for wildtype protein.]] |
+ | | [[Image:GLA_Wt_hbip.png|thumb|100px|Figure 43: Internal hydrogen bonds over time for wildtype protein.]] |
− | | [[Image:GLA_3_hbip.png|thumb|100px|Internal hydrogen bonds over time for mutation 3 protein.]] |
+ | | [[Image:GLA_3_hbip.png|thumb|100px|Figure 44: Internal hydrogen bonds over time for mutation 3 protein.]] |
− | | [[Image:GLA_8_hbip.png|thumb|100px|Internal hydrogen bonds over time for mutation 8 protein.]] |
+ | | [[Image:GLA_8_hbip.png|thumb|100px|Figure 45: Internal hydrogen bonds over time for mutation 8 protein.]] |
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− | | [[Image:GLA_Wt_hbpw.png|thumb|100px|Hydrogen bonds between protein and surrounding solvents for wildtype protein.]] |
+ | | [[Image:GLA_Wt_hbpw.png|thumb|100px|Figure 46: Hydrogen bonds between protein and surrounding solvents for wildtype protein.]] |
− | | [[Image:GLA_3_hbpw.png|thumb|100px|Hydrogen bonds between protein and surrounding solvents for mutation 3 protein.]] |
+ | | [[Image:GLA_3_hbpw.png|thumb|100px|Figure 47: Hydrogen bonds between protein and surrounding solvents for mutation 3 protein.]] |
− | | [[Image:GLA_8_hbpw.png|thumb|100px|Hydrogen bonds between protein and surrounding solvents for mutation 8 protein.]] |
+ | | [[Image:GLA_8_hbpw.png|thumb|100px|Figure 48: Hydrogen bonds between protein and surrounding solvents for mutation 8 protein.]] |
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! Mutation 8 |
! Mutation 8 |
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− | | [[Image:General_ramachandranplot_BCKDHA.png|thumb|100px|General ramachandran plot.<ref name=rama_wiki>http://en.wikipedia.org/wiki/Ramachandran_plot</ref>]] |
+ | | [[Image:General_ramachandranplot_BCKDHA.png|thumb|100px|Figure 49: General ramachandran plot.<ref name=rama_wiki>http://en.wikipedia.org/wiki/Ramachandran_plot</ref>]] |
− | | [[Image:GLA_Wt_rama.png|thumb|100px|Internal hydrogen bonds over time for wildtype protein.]] |
+ | | [[Image:GLA_Wt_rama.png|thumb|100px|Figure 50: Internal hydrogen bonds over time for wildtype protein.]] |
− | | [[Image:GLA_3_rama.png|thumb|100px|Internal hydrogen bonds over time for mutation 3 protein.]] |
+ | | [[Image:GLA_3_rama.png|thumb|100px|Figure 51: Internal hydrogen bonds over time for mutation 3 protein.]] |
− | | [[Image:GLA_8_rama.png|thumb|100px|Internal hydrogen bonds over time for mutation 8 protein.]] |
+ | | [[Image:GLA_8_rama.png|thumb|100px|Figure 52: Internal hydrogen bonds over time for mutation 8 protein.]] |
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− | | [[Image:GLA_Wt_rmsdmat.png|thumb|100px|RMSD matrix for wildtype protein.]] |
+ | | [[Image:GLA_Wt_rmsdmat.png|thumb|100px|Figure 53: RMSD matrix for wildtype protein.]] |
− | | [[Image:GLA_3_rmsdmat.png|thumb|100px|RMSD matrix for mutation 3 protein.]] |
+ | | [[Image:GLA_3_rmsdmat.png|thumb|100px|Figure 54: RMSD matrix for mutation 3 protein.]] |
− | | [[Image:GLA_8_rmsdmat.png|thumb|100px|RMSD matrix for mutation 8 protein.]] |
+ | | [[Image:GLA_8_rmsdmat.png|thumb|100px|Figure 55: RMSD matrix for mutation 8 protein.]] |
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− | | [[Image:GLA_Wt_rmsdist.png|thumb|100px|RMS distribution for wildtype protein.]] |
+ | | [[Image:GLA_Wt_rmsdist.png|thumb|100px|Figure 56: RMS distribution for wildtype protein.]] |
− | | [[Image:GLA_3_rmsdist.png|thumb|100px|RMS distribution for mutation 3 protein.]] |
+ | | [[Image:GLA_3_rmsdist.png|thumb|100px|Figure 57: RMS distribution for mutation 3 protein.]] |
− | | [[Image:GLA_8_rmsdist.png|thumb|100px|RMS distribution for mutation 8 protein.]] |
+ | | [[Image:GLA_8_rmsdist.png|thumb|100px|Figure 58: RMS distribution for mutation 8 protein.]] |
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− | | [[Image:GLA_Wt_clusterpm.png|thumb|100px|Image of the largest two clusters of wildtype protein.]] |
+ | | [[Image:GLA_Wt_clusterpm.png|thumb|100px|Figure 59: Image of the largest two clusters of wildtype protein.]] |
− | | [[Image:GLA_3_clusterpm.png|thumb|100px|Image of the largest two clusters of mutation 3 protein.]] |
+ | | [[Image:GLA_3_clusterpm.png|thumb|100px|Figure 60: Image of the largest two clusters of mutation 3 protein.]] |
− | | [[Image:GLA_8_clusterpm.png|thumb|100px|Image of the largest two clusters of mutation 8 protein.]] |
+ | | [[Image:GLA_8_clusterpm.png|thumb|100px|Figure 61: Image of the largest two clusters of mutation 8 protein.]] |
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− | | [[Image:GLA_Wt_rmsdev.png|thumb|100px|RMS deviation for wildtype protein.]] |
+ | | [[Image:GLA_Wt_rmsdev.png|thumb|100px|Figure 62: RMS deviation for wildtype protein.]] |
− | | [[Image:GLA_3_rmsdev.png|thumb|100px|RMS deviation for mutation 3 protein.]] |
+ | | [[Image:GLA_3_rmsdev.png|thumb|100px|Figure 63: RMS deviation for mutation 3 protein.]] |
− | | [[Image:GLA_8_rmsdev.png|thumb|100px|RMS deviation for mutation 8 protein.]] |
+ | | [[Image:GLA_8_rmsdev.png|thumb|100px|Figure 64: RMS deviation for mutation 8 protein.]] |
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Revision as of 20:10, 16 October 2011
by Benjamin Drexler and Fabian Grandke
Contents
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.
Methods/Materials
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 |
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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 |
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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 |
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-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 |
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Plot |
Quality assurance
Convergence of energy terms
Temperature
Description | Wildtype | Mutation 3 | Mutation 8 |
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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 |
Pressure
Description | Wildtype | Mutation 3 | Mutation 8 |
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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 |
Potential
Description | Wildtype | Mutation 3 | Mutation 8 |
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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 |
Total Energy
Description | Wildtype | Mutation 3 | Mutation 8 |
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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 |
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 |
Root mean square fluctuations
Description | Wildtype | Mutation 3 | Mutation 8 |
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Plot | |||
Plot | |||
Plot | |||
Plot |
Convergence of radius of gyration
Description | Wildtype | Mutation 3 | Mutation 8 |
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Plot |
Solvent accessible surface area
Description | Wildtype | Mutation 3 | Mutation 8 |
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Plot | |||
Plot | |||
Plot |
Hydrogen bonds
Description | Wildtype | Mutation 3 | Mutation 8 |
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Plot | |||
Plot |
Ramachandran (phi/psi) plots
General Ramachandran | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
![]() Figure 49: General ramachandran plot.<ref name=rama_wiki>http://en.wikipedia.org/wiki/Ramachandran_plot</ref> |
Analysis of dynamics and time-averaged properties
Root mean square deviations again
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Plot |
Cluster analysis
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Plot | |||
Plot |
Distance RMSD
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Plot |
References
<references />