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Molecular Mechanics MM and Molecular Dynamics MD (Read 7497 times)
Gerrit-Jan Linker
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Molecular Mechanics MM and Molecular Dynamics MD
04.12.08 at 13:03:46
 
Molecular Mechanics MM and Molecular Dynamics MD
 
MM - Molecular Mechanics
 
The term molecular mechanics refers to the use of Newtonian mechanics to model molecular systems. The potential energy of all systems in molecular mechanics is calculated using force fields.
 
The prototypical Molecular Mechanics application is energy minimization. That is, the force field is used as an optimization criterion and the (local) minimum searched by an appropriate algorithm
 
MD - Molecular Dynamics
 
Molecular dynamics (MD) is a form of computer simulation in which atoms and molecules are allowed to interact for a period of time by approximations of known physics, giving a view of the motion of the atoms.
 
Molecular Mechanics and Molecular Dynamics (MD) are related but different. Main purpose of MD is modeling of molecular motions, although it is also applied for optimization, for example using simulated annealing. MM implements more "static" energy minimization methods to study the potential energy surfaces of different molecular systems. However, MM can also provide important dynamic parameters, such as energy barriers between different conformers or steepness of a potential energy surface around a local minimum. MD and MM are usually based on the same classical force fields.
 
Sources:
MD
http://en.wikipedia.org/wiki/Molecular_dynamics
MM
http://en.wikipedia.org/wiki/Molecular_mechanics
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Gerrit-Jan Linker
Linker IT Software
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Gerrit-Jan Linker
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Definition of a model for molecular simulations
Reply #1 - 27.05.10 at 08:27:32
 
Definition of a model for molecular simulations
 
Molecular model constists of:
 
  • Degrees of freedom:  
    atom are the elementary particles.
     
  • Boundary conditions:  
    system temperatur, pressure, walls, external forces.
     
  • Forces or interactions between atoms.  
    Force field = physico-chemical knowledge.
     
    There is a close link between potential and frequency. The time required to traverse the potential is dependent on the shape of the potential and the mass.
     
  • Methods to generate configurations of atoms:  
    Newton. F = m.a

 
Realism of MM and MD:
 

  • Accessibility of phase space
    All relevant conformations must be accessible during the simulation. The boundaries between them should not be too large.
  • Use tricks to search for other local minimum free energy regions
  • Quality and resolution of experimental data

 
 
Aim and scope of Simulation
  • Obtain a representative sample of the realisations of the system. Consider structural realisations and dynamical realisations.
  • The phase space (r,p) to be sampled depends on the degrees of freedom, scale of the system, time scale. Realism will depend on the judiciousness of our choice of these parameters.
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« Last Edit: 27.05.10 at 09:40:38 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
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