FF4_parameterization_handout

FF4_parameterization_handout - Force Fields Practical...

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1 Force Fields: Practical Aspects and Parameterization BIOL 7110 / CHEM 8901 / BIOL 4105 / CHEM 4804 March 3, 2011 Force Fields: The Goals GOAL 1: Given a molecular conformation, calculate the internal energy E as accurately as possible. If the energy function were perfectly accurate, we would be able to simulate all the conformational, thermodynamic, and kinetic properties of the system. E = f(x1,y1,z 1 ,…,x N ,y N ,z N ) $$$ Force Fields: The Goals GOAL 2: Force fields should be based, as far as possible, on first principles. GOAL 3: Force fields should be transferable . Parameters developed for one molecule (or class of molecules) should be applicable to as many different molecules (or classes of molecules) as possible. We shouldn’t have to develop a whole new set of parameters every time we begin to study a new molecule (or class of molecule) GOAL 1: Given a molecular conformation, calculate the internal energy E as accurately as possible.
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2 Force Fields: Reality Checks REALITY : Molecules are quantum mechanical systems. REALITY : It is impossible to solve Schrödinger’s equation analytically, and solving it numerically is very expensive. REALITY : In many cases when two or more biological macromolecules interact, quantum effects are of secondary importance. In particular, quantum effects do not contribute significantly to the energy differences between different conformations. (But if we choose to ignore quantum effects, we cannot simulate any of the actual biochemistry.) REALITY : There are competing demands on computer time: Force Fields: Reality Checks REALITY : There are competing demands on computer time: Molecular Mechanics Force Fields: The Compromises 1. Model molecules using classical mechanics (ignore QM)
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