computer modeling in molecular biology.pdf
computer modeling in molecular biology.pdf
computer modeling in molecular biology.pdf
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Computer Modell<strong>in</strong>g <strong>in</strong> Molecular BiologyEdited by Julia M . GoodfellowOVCH Verlagsgesellschaft mbH. 19956 Theory of Transport <strong>in</strong> Ion ChannelsFrom Molecular Dynamics Simulationsto ExperimentsBenoit RouxGroupe de Recherche en Transport MembranaireDCpartement de Physique. UniversitC de Montreal C.P. 6128. succ . ACanada H3C 3 57. CanadaContents6.1 Introduction ...................................................... 1346.2 Traditional Phenomenological Descriptions ........................... 1376.36.3.16.3.1.16.3.1.26.3.1.36.3.26.3.2.16.3.2.26.3.2.36.3.2.46.3.36.3.3.16.3.3.26.3.46.3.4.16.3.4.26.3.4.36.3.56.3.5.1The Gramicid<strong>in</strong> A Channel: A Model System for Molecular Dynamics ... 140The Potential Energy Function ...................................... 140Ab Znitio Calculations ............................................. 141Functional Form and Parametrization ................................ 141Limitations of the Potential Energy Function ......................... 142The Water-Filled Channel .......................................... 143Build<strong>in</strong>g the Initial System .......................................... 145Analysis of the Trajectory .......................................... 146147149150Rotational Mobility of Internal Water Molecules ......................Rare Events: Ethanolam<strong>in</strong>e Tail Isomerization .........................Calculation of the Potential of Mean Force: Free Energy Simulation .....Application and Techniques ......................................... 151Analysis of the Results. ............................................Calculation of a Transition Rate: Activated Dynamics Technique ........153155Application and Techniques ......................................... 156Analysis of the Results ............................................. 157Comparison with Experiments ...................................... 160Relation Between NP and ERT ...................................... 161Analysis of the Results ............................................. 1636.4 Conclusions ....................................................... 164References ........................................................ 166
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