EM_1 - 2/17/11 Introduction to Energy Minimization BIOL...

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2/17/11 1 Introduction to Energy Minimization BIOL 7110 / CHEM 8901 / BIOL 4105 / CHEM 4804 February 17, 2011 The semi-harmonic restraint K = 10 kcal/(mol•Å 2 ) and k box = 10Å. Used as the “box” restraint in Oscar
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2/17/11 2 The semi-harmonic restraint K = 10 kcal/(mol•Å 2 ) and k box = 10Å. This is an example of a one-dimensional energy surface. One-dimensional potential energy surface: n-butane E( φ ) (kcal/mol) E( φ ) = 2.5 + (7/6)*cos( φ ) + 0.5*cos(2 φ ) + (11/6)*cos(3 φ ) φ (deg)
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2/17/11 3 Two-Dimensional Energy Surfaces Energy Minimization: • a conformational search algorithm • an optimization algorithm
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2/17/11 4 Conformational Searches Goal: To find the lowest energy structure Approach: Calculate energy for different conformations Question: How to vary the conformation? Different search algorithms have different rules Optimization of the Structure Assumption: the optimal structure is the structure that has the lowest energy as calculated by the potential energy function . The energy surface is very complex, even for small molecules. The development of optimization algorithms is an area of major ongoing research efforts. The conformational energy surface is a 3N-dimensional surface. Optimization problem is confounded by the multiple minimum problem .
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2/17/11 5 Search Algorithm #1 Sample problem: What is the lowest point on Mars? Search strategy 1: Grid Search This is a reasonable strategy for this problem, because: • you can cover the surface completely with a grid of reasonable fineness • it’s a 2D search surface • The continuous function h(x,y) is well behaved
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This note was uploaded on 09/22/2011 for the course BIOL 7110 taught by Professor Steveharvey during the Spring '11 term at Georgia Institute of Technology.

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EM_1 - 2/17/11 Introduction to Energy Minimization BIOL...

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