Difference between revisions of "Molecular Dynamics Analysis GLA"
From Bioinformatikpedia
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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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+ | |||
− | * 2001 frames |
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+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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− | * time resolution of 5ps |
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+ | |- |
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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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+ | |2001 frames |
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+ | |2001 frames |
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+ | |2001 frames |
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+ | |- |
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+ | | time resolution of 5ps|| time resolution of 5ps|| time resolution of 5ps |
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+ | |- |
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+ | |} |
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'''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?''' |
'''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?''' |
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− | *18h06:37 |
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− | *13.252 ns/day |
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− | *~206740 years |
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+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
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− | '''Which contribution to the potential energy accounts for most of the calculations?''' |
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+ | |- |
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− | *-8.52573e+05 kJ/mol |
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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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+ | |18h06:37 ||18h29:13 ||18h19:11 |
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+ | |- |
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+ | | 13.252 ns/day|| 12.982 ns/day|| 13.101 ns/day |
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+ | |- |
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+ | | ~206740 years|| ~211040 years|| ~209123 years |
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+ | |- |
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+ | |} |
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− | ===Visualization of the results=== |
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− | ===Quality assurance=== |
||
− | ====Convergence of energy terms==== |
||
− | ==== Interaction Energy: Coulomb ==== |
||
− | ====Interaction Energy: Van der Waals ==== |
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− | ====Minimum distances between periodic images==== |
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− | ====Root mean square fluctuations==== |
||
− | ====Convergence of RMSD==== |
||
− | ====Convergence of radius of gyration==== |
||
− | === Structural analysis: properties derived from configurations === |
||
− | ==== Solvent accessible surface area ==== |
||
− | ====Hydrogen bonds==== |
||
− | ====Salt bridges==== |
||
− | ====Ramachandran (phi/psi) plots===== |
||
− | === Analysis of dynamics and time-averaged properties === |
||
− | ==== Root mean square deviations again ==== |
||
− | ====Cluster analysis==== |
||
− | ====Distance RMSD==== |
||
− | |||
− | ==Mutation 3== |
||
− | ===Brief check of the results=== |
||
− | '''How many frames are in the trajectory file and what is the time resolution?''' |
||
− | * 2001 frames |
||
− | * 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?''' |
||
− | *18h29:13 |
||
− | *12.982 ns/day |
||
− | *~211040 years |
||
'''Which contribution to the potential energy accounts for most of the calculations?''' |
'''Which contribution to the potential energy accounts for most of the calculations?''' |
||
+ | {|class="wikitable" border="1" style="text-align:center; border-spacing:0;" |
||
− | *-8.53327e+05 kJ/mol |
||
+ | |- |
||
+ | ! Wildtype |
||
+ | ! Mutation 3 |
||
+ | ! Mutation 8 |
||
+ | |- |
||
+ | | -8.52573e+05 kJ/mol|| -8.53327e+05 kJ/mol || -8.52539e+05 kJ/mol |
||
+ | |- |
||
+ | |} |
||
===Visualization of the results=== |
===Visualization of the results=== |
||
Line 73: | Line 72: | ||
====Distance RMSD==== |
====Distance RMSD==== |
||
− | ==Mutation 8== |
||
− | ===Brief check of the results=== |
||
− | '''How many frames are in the trajectory file and what is the time resolution?''' |
||
− | *2001 frames |
||
− | *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?''' |
||
− | *18h19:11 |
||
− | *13.101 ns/day |
||
− | *~209123 years |
||
− | |||
− | '''Which contribution to the potential energy accounts for most of the calculations?''' |
||
− | *-8.52539e+05 kJ/mol |
||
− | |||
− | ===Visualization of the results=== |
||
− | ===Quality assurance=== |
||
− | ====Convergence of energy terms==== |
||
− | ==== Interaction Energy: Coulomb ==== |
||
− | ====Interaction Energy: Van der Waals ==== |
||
− | ====Minimum distances between periodic images==== |
||
− | ====Root mean square fluctuations==== |
||
− | ====Convergence of RMSD==== |
||
− | ====Convergence of radius of gyration==== |
||
− | === Structural analysis: properties derived from configurations === |
||
− | ==== Solvent accessible surface area ==== |
||
− | ====Hydrogen bonds==== |
||
− | ====Salt bridges==== |
||
− | ====Ramachandran (phi/psi) plots===== |
||
− | === Analysis of dynamics and time-averaged properties === |
||
− | ==== Root mean square deviations again ==== |
||
− | ====Cluster analysis==== |
||
− | ====Distance RMSD==== |
||
= References = |
= References = |
Revision as of 23:08, 8 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
Wildtype
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
Interaction Energy: Coulomb
Interaction Energy: Van der Waals
Minimum distances between periodic images
Root mean square fluctuations
Convergence of RMSD
Convergence of radius of gyration
Structural analysis: properties derived from configurations
Solvent accessible surface area
Hydrogen bonds
Salt bridges
Ramachandran (phi/psi) plots=
Analysis of dynamics and time-averaged properties
Root mean square deviations again
Cluster analysis
Distance RMSD
References
<references />