Some practical aspects of free energy calculations from molecular dynamics simulation. - Srikanta Sen; Lennart Nilsson (J. Comput. Chem., 1999)

Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations. - Pekka Mark; Lennart Nilsson (J. Comput. Chem., 2002)

Improved precision and efficiency of free energy calculations for small systems using lambda-scaled atomic masses and separating conformational and transformational sampling. - Peter Carlsson; Lennart Nilsson (J. Comput. Chem., 2003)

A Highly Efficient Ab Initio Tight-Binding-Like Approximate Density-Functional Quantum Mechanical Method. - Yaoquan Tu; Lennart Nilsson; Aatto Laaksonen (PARA, 2006)

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)

Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations. - Lennart Nilsson (J. Comput. Chem., 2009)

How Thioredoxin Dissociates Its Mixed Disulfide. - Goedele Roos; Nicolas Foloppe; Koen Van Laer; Lode Wyns; Lennart Nilsson; Paul Geerlings; Joris Messens (PLoS Comput. Biol., 2009)

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA. - Elizabeth J. Denning; U. Deva Priyakumar; Lennart Nilsson; Alexander D. MacKerell Jr. (J. Comput. Chem., 2011)

Conformational Preferences of Modified Uridines: Comparison of AMBER Derived Force Fields. - Indrajit Deb; Joanna Sarzynska; Lennart Nilsson; Ansuman Lahiri (J. Chem. Inf. Model., 2014)

Additive CHARMM force field for naturally occurring modified ribonucleotides. - You Xu; Kenno Vanommeslaeghe; Alexey Aleksandrov; Alexander D. MacKerell Jr.; Lennart Nilsson (J. Comput. Chem., 2016)

The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid. - You Xu; Alessandra Villa; Lennart Nilsson (J. Comput. Chem., 2017)

Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids. - Yossa Dwi Hartono; You Xu; Andrey Karshikoff; Lennart Nilsson; Alessandra Villa (J. Chem. Inf. Model., 2018)