Difference between revisions of "Molecular Dynamics Analysis GLA"

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m (Brief check of the results)
m
Line 10: Line 10:
   
 
'''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?'''
  +
* 2001 frames
 
  +
{|class="wikitable" border="1" style="text-align:center; border-spacing:0;"
* time resolution of 5ps
 
  +
|-
  +
! 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?'''
 
'''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?'''
*18h06:37
 
*13.252 ns/day
 
*~206740 years
 
   
  +
{|class="wikitable" border="1" style="text-align:center; border-spacing:0;"
'''Which contribution to the potential energy accounts for most of the calculations?'''
 
  +
|-
*-8.52573e+05 kJ/mol
 
  +
! 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
  +
|-
  +
|}
   
===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====
 
 
==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 22:08, 8 October 2011

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.

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 />