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MD: Molecular Dynamics (Read 1712 times)
Gerrit-Jan Linker
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MD: Molecular Dynamics
21.06.10 at 13:27:13
 
MD: Molecular Dynamics
 
For an introduction on MD I refer to:
Molecular Mechanics MM and Molecular Dynamics MD  
http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1228392226
 
Notes on MD:
 

  • Timescales
    Time required to cross a free energy barrier:
    τ = τ0exp(ΔG/kBT)
                                  1 kcal/mol ~ ps ; 5 kcal/mol ~ ns ; 10 kcal/mol ~ μs
    Sampling should exceed the timescales by ~ 10 fold.
     
  • Thermodynamic variables T and P
    • Statistical ensembles connect microscopic to macroscopic
      Microcanonical (NVE, Entropy)
      Canonical (NVT, Helmholz free energy)
      Isothermic-isobaric (NPT, Gibbs free energy)
    • Thermostats, barostats allow to choose the appropriate ensemble.
      (Andersen, Nose, Hoover)

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« Last Edit: 21.06.10 at 13:35:03 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
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