Difference between revisions of "Molecular Dynamics Analysis GLA"

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(Brief check of the results)
(Brief check of the results)
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==Mutation 3==
 
==Mutation 3==
 
===Brief check of the results===
 
===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
  +
*211040,365690746
  +
  +
'''Which contribution to the potential energy accounts for most of the calculations?'''
  +
*-8.53327e+05 kJ/mol
  +
 
===Visualization of the results===
 
===Visualization of the results===
 
===Quality assurance===
 
===Quality assurance===

Revision as of 07:24, 23 September 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?

  • 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?

  • 18h06:37
  • 13.252
  • 206740,569528921

Which contribution to the potential energy accounts for most of the calculations?

  • -8.52573e+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

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
  • 211040,365690746

Which contribution to the potential energy accounts for most of the calculations?

  • -8.53327e+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

Mutation 8

Brief check of the results

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

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