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Biochemistry, Biophysics, and Structural Biology Commons

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Retrospective Theses and Dissertations

2006

Applied mathematics

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A Penalty Function Method For Constrained Molecular Dynamics , Ajith Gunaratne Jan 2006

A Penalty Function Method For Constrained Molecular Dynamics , Ajith Gunaratne

Retrospective Theses and Dissertations

We propose a penalty-function method for constrained molecular dynamic simulation by defining a quadratic penalty function for the constraints. The simulation with such a method can be done by using a conventional, unconstrained solver only with the penalty parameter increased in an appropriate manner as the simulation proceeds. More specifically, we scale the constraints with their force constants when forming the penalty terms. The resulting force function can then be viewed as a smooth continuation of the original force field as the penalty parameter increases. The penalty function method is easy to implement and costs less than a Lagrange multiplier ...