Thomas E. Cheatham

The Amber biomolecular simulation programs

Abstract We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program...

Calculating Structures and Free Energies of Complex Molecules:  Combining Molecular Mechanics and Continuum Models

A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent developments combining state-of-the-art force fields wit...

AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise

In the last five years we have witnessed a significant increase in the number publications describing accurate and reliable all-atom molecular dynamics simulations of nucleic ac...

Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program