Corfrmational Energy Searching

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        02:22 PM, July 20, 2007
      
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        Corfrmational Energy Searching
      
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        Energy is a function of the degrees of freedom in a molecule (i.e. bonds, angles, and 
        dihedrals). Conformational energy searching is used to find all of the energetically 
        preferred conformations of a molecule (especially rotamers), which is 
      
      
        <b>mathematically equivalent to locating all of the minima of its energy function. </b>
      
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        <b>An energy surface resembles a mountain range, complete with peaks (energy barriers), 
        valleys (energy minima), and passes (saddle points</b>
      
      
        ). 
      
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        Molecular mechanics energy approximations are most valid in and around the minima. The 
        lowest energy minima tend to be the most populated (as per the Boltzmann distributio
      
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        Energy minimization methods can precisely locate minimum energy conformations by 
        mathematically "homing in" on the energy function minima (one at a time). The goal of 
        energy minimization is to find a route (consisting of variation of the intramolecular 
        degrees of freedom) from an initial conformation to the nearest minimum energy 
        conformation using the smallest number of calculations possible. Note that, unlike 
        molecular dynamics, the steps between starting and minimum energy conformations have no 
        physical meaning in energy minimization.
      
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        Energy minimization methods can precisely locate minimum energy conformations by 
      
      
        <b>mathematically "homing in" on the energy function minima (one at a time). </b>
      
      
        The goal of energy minimization is to find a route (consisting of variation of the 
        intramolecular degrees of freedom) from an initial conformation to the nearest minimum 
        energy conformation using the smallest number of calculations possible. Note that, unlike 
        molecular dynamics, the steps between starting and minimum energy conformations have no 
        physical meaning in energy minimization.
      
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        Minimization algorithms are designed to
      
      
        <b> head down-hill toward the nearest minimum</b>
      
      
        . 
      
      
        <b>Remote minima (separated from the initial conformation by an energy barrier) </b>
      
      
        are not detected by energy minimization because this would 
      
      
        <b>require some period of up-hill movement</b>
      
      
        
      
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Corfrmational Energy Searching

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