Fast Energy Minimization of large Polymers Using Constrained Optimization

A new computational technique is described that uses distance constraints to calculate empirical potential energy minima of partially rigid molecules. A constrained minimuzation algorithm that works entirely in Cartesian coordinates is used. The algorithm does not obey the constraints until convergence, a feature that reduces ill-conditioning and allows constrained local minima to be computed more quickly than unconstrained minima. Computational speedup exceeds the 3-fold factor commonly obtained in constained molecular dynamics simulations, where the constraints must be strictly obeyed at all times