FF2 - 1 Representing Molecules on a Computer I The...

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Unformatted text preview: 1 Representing Molecules on a Computer: I. The Macromolecular Potential Energy Function BIOL 7110 / CHEM 8901 / BIOL 4105 / CHEM 4804 February 24, 2011 Molecular Mechanics Input to a molecular dynamics program: A set of molecular x,y,z coordinates An energy function An algorithm E = f(x 1 ,y 1 ,z 1 ,…,x N ,y N ,z N ) x’ = f(x) How does the information in the molecular energy function get into the computer? PDB file, read by computer Programmed into the computer Breakdown of Molecular Energy Function Into Bonded and Nonbonded Terms E = E bonded + E nonbonded E bonded = E bonds + E angles + E torsions + E improper torsions E nb = E van der Waals + E Electrostatic E nb : interactions between atoms separated by many bonds, but close in space E bonded : interactions between atoms separated by 1, 2 or 3 bonds 2 Molecular Energy Function: The Bonded Terms E bonded = E bonds + E angles + E torsions + E improper torsions E bonded : interactions between atoms separated by 1, 2 or 3 bonds Bond Stretching Treated Like a Classical Spring (Hooke’s Law = Harmonic Approximation) (Reality is closer to a Morse Potential) The Harmonic Bond Energy Term Gives A Normal Distribution of Bond Lengths The bond energy term is harmonic (“harmonic” = quadratic in the independent variable) The bond length probability distribution is given by the Boltzmann equation...
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FF2 - 1 Representing Molecules on a Computer I The...

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