Difference between revisions of "Molecular Dynamics Analysis GLA"
From Bioinformatikpedia
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=Results= |
=Results= |
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+ | ==Brief check of the results== |
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− | ==Wildtype== |
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− | ===Brief check of the results=== |
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'''How many frames are in the trajectory file and what is the time resolution?''' |
'''How many frames are in the trajectory file and what is the time resolution?''' |
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− | + | ==Visualization of the results== |
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− | + | ==Quality assurance== |
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− | + | ===Convergence of energy terms=== |
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− | ==== |
+ | ====Temperature==== |
+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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− | ====Interaction Energy: Van der Waals ==== |
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+ | |- |
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− | ====Minimum distances between periodic images==== |
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+ | ! Description |
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− | ====Root mean square fluctuations==== |
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+ | ! Wildtype |
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− | ====Convergence of RMSD==== |
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+ | ! Mutation 3 |
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− | ====Convergence of radius of gyration==== |
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+ | ! Mutation 8 |
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− | === Structural analysis: properties derived from configurations === |
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+ | |- |
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− | ==== Solvent accessible surface area ==== |
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+ | |Max(kJ/mol) || 0|| 0 || 0 |
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− | ====Hydrogen bonds==== |
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+ | |- |
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− | ====Salt bridges==== |
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+ | |Min(kJ/mol) || 0|| 0 || 0 |
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− | ====Ramachandran (phi/psi) plots===== |
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+ | |- |
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− | === Analysis of dynamics and time-averaged properties === |
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+ | |Average(kJ/mol) || 0|| 0 || 0 |
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− | ==== Root mean square deviations again ==== |
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+ | |- |
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− | ====Cluster analysis==== |
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+ | |Plot |
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− | ====Distance RMSD==== |
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+ | | [[Image:GLA_Wt_temp.png|thumb|100px|Temperature over time for wildtype.]] |
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+ | | [[Image:GLA_3_temp.png|thumb|100px|Temperature over time for mutation 3.]] |
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+ | | [[Image:GLA_8_temp.png|thumb|100px|Temperature over time for mutation 8.]] |
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+ | |- |
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+ | |} |
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+ | |||
+ | ====Pressure==== |
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+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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+ | |- |
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+ | ! Description |
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+ | ! Wildtype |
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+ | ! Mutation 3 |
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+ | ! Mutation 8 |
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+ | |- |
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+ | |Max(kJ/mol) || 0|| 0 || 0 |
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+ | |- |
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+ | |Min(kJ/mol) || 0|| 0 || 0 |
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+ | |- |
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+ | |Average(kJ/mol) || 0|| 0 || 0 |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_pressure.png|thumb|100px|Pressure over time for wildtype.]] |
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+ | | [[Image:GLA_3_pressure.png|thumb|100px|Pressure over time for mutation 3.]] |
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+ | | [[Image:GLA_8_pressure.png|thumb|100px|Pressure over time for mutation 8.]] |
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+ | |- |
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+ | |} |
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+ | ====Potential==== |
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+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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+ | |- |
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+ | ! Description |
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+ | ! Wildtype |
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+ | ! Mutation 3 |
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+ | ! Mutation 8 |
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+ | |- |
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+ | |Max(kJ/mol) || 0|| 0 || 0 |
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+ | |- |
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+ | |Min(kJ/mol) || 0|| 0 || 0 |
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+ | |- |
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+ | |Average(kJ/mol) || 0|| 0 || 0 |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_potent.png|thumb|100px|Potential over time for wildtype.]] |
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+ | | [[Image:GLA_3_potent.png|thumb|100px|Potential over time for mutation 3.]] |
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+ | | [[Image:GLA_8_potent.png|thumb|100px|Potential over time for mutation 8.]] |
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+ | |- |
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+ | |} |
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+ | ====Total Energy==== |
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+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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+ | |- |
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+ | ! Description |
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+ | ! Wildtype |
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+ | ! Mutation 3 |
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+ | ! Mutation 8 |
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+ | |- |
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+ | |Max(kJ/mol) || 0|| 0 || 0 |
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+ | |- |
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+ | |Min(kJ/mol) || 0|| 0 || 0 |
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+ | |- |
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+ | |Average(kJ/mol) || 0|| 0 || 0 |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_ener.png|thumb|100px|Total energy over time for wildtype.]] |
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+ | | [[Image:GLA_3_ener.png|thumb|100px|Total energy over time for mutation 3.]] |
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+ | | [[Image:GLA_8_ener.png|thumb|100px|Total energy over time for mutation 8.]] |
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+ | |- |
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+ | |} |
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+ | |||
+ | ===Minimum distances between periodic images=== |
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+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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+ | |- |
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+ | ! Description |
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+ | ! Wildtype |
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+ | ! Mutation 3 |
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+ | ! Mutation 8 |
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+ | |- |
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+ | |Max(nm) || 0|| 0 || 0 |
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+ | |- |
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+ | |Min(nm) || 0|| 0 || 0 |
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+ | |- |
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+ | |Average(nm) || 0|| 0 || 0 |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_mindist.png|thumb|100px|Minimum distance between periodic boundary cells for wildtype.]] |
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+ | | [[Image:GLA_3_mindist.png|thumb|100px|Minimum distance between periodic boundary cells for mutation 3.]] |
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+ | | [[Image:GLA_8_mindist.png|thumb|100px|Minimum distance between periodic boundary cells for mutation 8.]] |
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+ | |- |
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+ | |} |
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+ | |||
+ | ===Root mean square fluctuations=== |
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+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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+ | |- |
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+ | ! Description |
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+ | ! Wildtype |
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+ | ! Mutation 3 |
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+ | ! Mutation 8 |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_rmsf.png|thumb|100px|Root mean square fluctuations for wildtype protein.]] |
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+ | | [[Image:GLA_3_rmsf.png|thumb|100px|Root mean square fluctuations for mutation 3 protein.]] |
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+ | | [[Image:GLA_8_rmsf.png|thumb|100px|Root mean square fluctuations for mutation 8 protein.]] |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_rmsfc.png|thumb|100px|Root mean square fluctuations for wildtype C-alpha.]] |
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+ | | [[Image:GLA_3_rmsfc.png|thumb|100px|Root mean square fluctuations for mutation 3 C-alpha.]] |
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+ | | [[Image:GLA_8_rmsfc.png|thumb|100px|Root mean square fluctuations for mutation 8 C-alpha.]] |
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+ | |- |
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+ | |} |
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+ | ===Convergence of radius of gyration=== |
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+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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+ | |- |
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+ | ! Description |
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+ | ! Wildtype |
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+ | ! Mutation 3 |
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+ | ! Mutation 8 |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_radius.png|thumb|100px|Radius of gyration over time for wildtype protein.]] |
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+ | | [[Image:GLA_3_radius.png|thumb|100px|Radius of gyration over time for mutation 3 protein.]] |
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+ | | [[Image:GLA_8_radius.png|thumb|100px|Radius of gyration over time for mutation 8 protein.]] |
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+ | |- |
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+ | |} |
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+ | |||
+ | === Solvent accessible surface area === |
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+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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+ | |- |
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+ | ! Description |
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+ | ! Wildtype |
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+ | ! Mutation 3 |
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+ | ! Mutation 8 |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_sas.png|thumb|100px|Solvent accessible surface area over time for wildtype protein.]] |
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+ | | [[Image:GLA_3_sas.png|thumb|100px|Solvent accessible surface area over time for mutation 3 protein.]] |
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+ | | [[Image:GLA_8_sas.png|thumb|100px|Solvent accessible surface area over time for mutation 8 protein.]] |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_sasa.png|thumb|100px|Solvent accessible surface area per atom for wildtype protein.]] |
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+ | | [[Image:GLA_3_sasa.png|thumb|100px|Solvent accessible surface area per atom for mutation 3 protein.]] |
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+ | | [[Image:GLA_8_sasa.png|thumb|100px|Solvent accessible surface area per atom for mutation 8 protein.]] |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_sasr.png|thumb|100px|Solvent accessible surface area per residue for wildtype protein.]] |
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+ | | [[Image:GLA_3_sasr.png|thumb|100px|Solvent accessible surface area per residue for mutation 3 protein.]] |
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+ | | [[Image:GLA_8_sasr.png|thumb|100px|Solvent accessible surface area per residue for mutation 8 protein.]] |
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+ | |- |
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+ | |} |
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+ | |||
+ | ===Hydrogen bonds=== |
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+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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+ | |- |
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+ | ! Description |
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+ | ! Wildtype |
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+ | ! Mutation 3 |
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+ | ! Mutation 8 |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_hbip.png|thumb|100px|Internal hydrogen bonds over time for wildtype protein.]] |
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+ | | [[Image:GLA_3_hbip.png|thumb|100px|Internal hydrogen bonds over time for mutation 3 protein.]] |
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+ | | [[Image:GLA_8_hbip.png|thumb|100px|Internal hydrogen bonds over time for mutation 8 protein.]] |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_hbpw.png|thumb|100px|Hydrogen bonds between protein and surrounding solvents for wildtype protein.]] |
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+ | | [[Image:GLA_3_hbpw.png|thumb|100px|Hydrogen bonds between protein and surrounding solvents for mutation 3 protein.]] |
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+ | | [[Image:GLA_8_hbpw.png|thumb|100px|Hydrogen bonds between protein and surrounding solvents for mutation 8 protein.]] |
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+ | |- |
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+ | |} |
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+ | |||
+ | ===Ramachandran (phi/psi) plots==== |
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+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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+ | |- |
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+ | ! General Ramachandran |
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+ | ! Wildtype |
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+ | ! Mutation 3 |
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+ | ! Mutation 8 |
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+ | |- |
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+ | | [[Image:General_ramachandranplot_BCKDHA.png|thumb|100px|General ramachandran plot.]] |
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+ | | [[Image:GLA_Wt_rama.png|thumb|100px|Internal hydrogen bonds over time for wildtype protein.]] |
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+ | | [[Image:GLA_3_rama.png|thumb|100px|Internal hydrogen bonds over time for mutation 3 protein.]] |
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+ | | [[Image:GLA_8_rama.png|thumb|100px|Internal hydrogen bonds over time for mutation 8 protein.]] |
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+ | |- |
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+ | |} |
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+ | == Analysis of dynamics and time-averaged properties == |
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+ | === Root mean square deviations again === |
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+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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+ | |- |
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+ | ! Description |
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+ | ! Wildtype |
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+ | ! Mutation 3 |
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+ | ! Mutation 8 |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_rmsdmat.png|thumb|100px|RMSD matrix for wildtype protein.]] |
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+ | | [[Image:GLA_3_rmsdmat.png|thumb|100px|RMSD matrix for mutation 3 protein.]] |
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+ | | [[Image:GLA_8_rmsdmat.png|thumb|100px|RMSD matrix for mutation 8 protein.]] |
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+ | |- |
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+ | |} |
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+ | ===Cluster analysis=== |
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+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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+ | |- |
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+ | ! Description |
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+ | ! Wildtype |
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+ | ! Mutation 3 |
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+ | ! Mutation 8 |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_rmsdist.png|thumb|100px|RMS distribution for wildtype protein.]] |
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+ | | [[Image:GLA_3_rmsdist.png|thumb|100px|RMS distribution for mutation 3 protein.]] |
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+ | | [[Image:GLA_8_rmsdist.png|thumb|100px|RMS distribution for mutation 8 protein.]] |
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+ | |- |
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+ | |} |
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+ | ===Distance RMSD=== |
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+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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+ | |- |
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+ | ! Description |
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+ | ! Wildtype |
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+ | ! Mutation 3 |
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+ | ! Mutation 8 |
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+ | |- |
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+ | |Plot |
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+ | | [[Image:GLA_Wt_rmsdev.png|thumb|100px|RMS deviation for wildtype protein.]] |
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+ | | [[Image:GLA_3_rmsdev.png|thumb|100px|RMS deviation for mutation 3 protein.]] |
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+ | | [[Image:GLA_8_rmsdev.png|thumb|100px|RMS deviation for mutation 8 protein.]] |
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+ | |- |
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+ | |} |
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= References = |
= References = |
Revision as of 15:56, 9 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 |
---|---|---|
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
Quality assurance
Convergence of energy terms
Temperature
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Max(kJ/mol) | 0 | 0 | 0 |
Min(kJ/mol) | 0 | 0 | 0 |
Average(kJ/mol) | 0 | 0 | 0 |
Plot |
Pressure
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Max(kJ/mol) | 0 | 0 | 0 |
Min(kJ/mol) | 0 | 0 | 0 |
Average(kJ/mol) | 0 | 0 | 0 |
Plot |
Potential
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Max(kJ/mol) | 0 | 0 | 0 |
Min(kJ/mol) | 0 | 0 | 0 |
Average(kJ/mol) | 0 | 0 | 0 |
Plot |
Total Energy
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Max(kJ/mol) | 0 | 0 | 0 |
Min(kJ/mol) | 0 | 0 | 0 |
Average(kJ/mol) | 0 | 0 | 0 |
Plot |
Minimum distances between periodic images
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Max(nm) | 0 | 0 | 0 |
Min(nm) | 0 | 0 | 0 |
Average(nm) | 0 | 0 | 0 |
Plot |
Root mean square fluctuations
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Plot | |||
Plot |
Convergence of radius of gyration
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Plot |
Solvent accessible surface area
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Plot | |||
Plot | |||
Plot |
Hydrogen bonds
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Plot | |||
Plot |
Ramachandran (phi/psi) plots=
General Ramachandran | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
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 |
Distance RMSD
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Plot |
References
<references />