Computer simulation of liquids
Computer simulation of liquids
TNPACK—A truncated Newton minimization package for large-scale problems: I. Algorithm and usage
ACM Transactions on Mathematical Software (TOMS)
A truncated Newton minimizer adapted for CHARMM and biomolecular applications
Journal of Computational Chemistry
Line search algorithms with guaranteed sufficient decrease
ACM Transactions on Mathematical Software (TOMS)
Remark on Algorithm 702—the updated truncated Newton minimization package
ACM Transactions on Mathematical Software (TOMS)
Efficient Implementation of the Truncated-Newton Algorithm for Large-Scale Chemistry Applications
SIAM Journal on Optimization
Molecular Modeling and Simulation: An Interdisciplinary Guide
Molecular Modeling and Simulation: An Interdisciplinary Guide
Numerical Methods for Unconstrained Optimization and Nonlinear Equations (Classics in Applied Mathematics, 16)
An incomplete Hessian Newton minimization method and its application in a chemical database problem
Computational Optimization and Applications
An effective compressed sparse preconditioner for large scale biomolecular simulations
CIS'04 Proceedings of the First international conference on Computational and Information Science
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This paper gives a general convergence analysis to the truncated incomplete Hessian Newton method (T-IHN). It shows that T-IHN is globally convergent even with an indefinite incomplete Hessian matrix or an indefinite preconditioner, which may happen in practice. It also proves that when the T-IHN iterates are close enough to a minimum point, T-IHN has a Q-linear rate of convergence, and an admissible line search steplength of one. Moreover, a particular T-IHN algorithm is constructed for minimizing a biomolecular potential energy function, and numerically tested for a protein model problem based on a widely used molecular simulation package, CHARMM. Numerical results confirm the theoretical results, and demonstrate that T-IHN can have a better performance (in terms of computer CPU time) than most CHARMM minimizers.