MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

Protein Thermostability Calculations Using Alchemical Free Energy Simulations

(2010) Daniel Seeliger et al.   BIOPHYSICAL JOURNAL

Simulaid: A simulation facilitator and analysis program

(2010) Mihaly Mezei   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open↔Closed Transitions

(2009) Oliver Beckstein et al.   JOURNAL OF MOLECULAR BIOLOGY

MD-TRACKS: A Productive Solution for the Advanced Analysis of Molecular Dynamics and Monte Carlo simulations

(2008) Toon Verstraelen et al.   Journal of Chemical Information and Modeling

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation