EM2_Conf_Search_SA - 2/22/11 Conformational Searches and...

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2/22/11 1 Conformational Searches and Optimization: Energy Minimization and Simulated Annealing BIOL 7110 / CHEM 8901 / BIOL 4105 / CHEM 4804 February 22, 2011 Energy Minimization on 10 Atoms of Lennard-Jonesium: Starting Configuration Convergence Criteria for Energy Minimization In complex systems like molecules, we cannot know the shape of the conformational energy surface. When carrying out energy minimization, when do we stop? There are several possible criteria for stopping: 1 – Minimize for a specified number of cycles 2a – when the average gradient falls below some pre-selected value 2 – Minimize until “convergence”, defined by 2b – when the change in energy falls below some pre-selected value
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2/22/11 2 Energy Minimization on LJ10 Energy Minimization on LJ10 Steepest Descent Energy Minimization on LJ10: Effect of the Convergence Criterion Δ E/E e-5 Δ Δ Δ E/E e-5 Δ E/E e-7 Δ E/E e-9
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2/22/11 3 Steepest Descent Energy Minimization on LJ10: Effect of the Convergence Criterion Conjugate Gradient Energy Minimization on LJ10 Energy Minimization on LJ10: Steepest Descent vs. Conjugate Gradient CG SD
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2/22/11 4 Energy Minimization on 10 Atoms of Lennard-Jonesium: Successive Minima and the Issue of Convergence How long do we keep going? How to define a criterion for quitting (“convergence”)? Energy Minimization on LJ10: Step Size Values reported at every step of minimization.
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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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EM2_Conf_Search_SA - 2/22/11 Conformational Searches and...

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