Difference between revisions of "Molecular Dynamics Simulations Analysis of Glucocerebrosidase"

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(Created page with "== Introduction == To analyze our Molecular Dynamics Simulations we followed the tutorial described here: http://md.chem.rug.nl/~mdcourse/analysis1.html == Wildtype == === A b…")
 
(→‎A brief check of results)
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=== A brief check of results ===
  
=== A brief check of results ===
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* command: <code>gmxcheck -f 2NT0_wt_md.xtc </code>
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'''How many frames are in the trajectory file and what is the time resolution?'''
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* 2001 frames
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* timestep: 5ps
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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?'''
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* Simulation run: 8h37:36
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* Simulation speed: 27.821
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* Time to reach a second: 1/0.000000028 = 35714285,714285714 days = 97847,358121331 years
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'''Which contribution to the potential energy accounts for most of the calculations?'''
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* -9.39801e+05 kJ/mol
   
 
=== Visualization of results ===
 
=== Visualization of results ===

Revision as of 07:54, 23 August 2011

Introduction

To analyze our Molecular Dynamics Simulations we followed the tutorial described here: http://md.chem.rug.nl/~mdcourse/analysis1.html

Wildtype

A brief check of results

  • command: gmxcheck -f 2NT0_wt_md.xtc

How many frames are in the trajectory file and what is the time resolution?

  • 2001 frames
  • timestep: 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?

  • Simulation run: 8h37:36
  • Simulation speed: 27.821
  • Time to reach a second: 1/0.000000028 = 35714285,714285714 days = 97847,358121331 years

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

  • -9.39801e+05 kJ/mol

Visualization of results

Quality assurance

Convergence of energy terms

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

Secondary structure

Ramachandran (phi/psi) plots

Analysis of dynamics and time-averaged properties

Root mean square deviations again

Cluster analysis

Distance RMSD

Mutation 7

still waiting


Mutation 10

still waiting


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