Algorithms for Constrained Molecular Dynamics. - Eric Barth; Krzysztof Kuczera; Benedict J. Leimkuhler; Robert D. Skeel (J. Comput. Chem., 1995)

One- and multidimensional conformational free energy simulations. - Krzysztof Kuczera (J. Comput. Chem., 1996)

Exploration of Peptide Free Energy Surfaces. - Krzysztof Kuczera (Computational Molecular Dynamics, 1999)

CHARMM: The biomolecular simulation program. - Bernard R. Brooks; Charles L. Brooks III; Alexander D. MacKerell Jr.; Lennart Nilsson; Robert J. Petrella; Benoît Roux; Y. Won; G. Archontis; Christian Bartels; Stefan Boresch; Amedeo Caflisch; Leo S. D. Caves; et al. (J. Comput. Chem., 2009)