PUPIL: A systematic approach to software integration in multi-scale simulations. - Juan Torras; Yao He; Chao Cao; Krishna Muralidharan; Erik Deumens; H.-P. Cheng; Samuel B. Trickey (Comput. Phys. Commun., 2007)

A versatile AMBER-Gaussian QM/MM interface through PUPIL. - Juan Torras; Gustavo de M. Seabra; Erik Deumens; Samuel B. Trickey; Adrian E. Roitberg (J. Comput. Chem., 2008)

Incorporation of deMon2k as a new parallel quantum mechanical code for the PUPIL system. - Oscar Bertran; Samuel B. Trickey; Juan Torras (J. Comput. Chem., 2010)

Parameterization of the torsional potential for calix[4]arene-substituted poly(thiophene)s. - Julien Preat; Francisco Rodríguez-Ropero; Juan Torras; Oscar Bertran; David Zanuy; Carlos Alemán (J. Comput. Chem., 2010)

Comment on "a minimal implementation of the AMBER-GAUSSIAN interface for Ab Initio QM/MM-MD simulation". - Benjamin P. Roberts; Gustavo de M. Seabra; Adrian E. Roitberg; Kenneth M. Merz Jr.; Erik Deumens; Juan Torras; Samuel B. Trickey (J. Comput. Chem., 2012)

IgG1-b12-HIV-gp120 Interface in Solution: A Computational Study. - Didac Martí; Carlos Alemán; Jon Ainsley; Oscar Ahumada; Juan Torras (J. Chem. Inf. Model., 2022)

Intelligent cross-linking in polymer simulations: SuSi's approach to complex 3D networks. - David Naranjo; Didac Martí; Carlos Alemán; Jose Garcia-Torres; Juan Torras (Comput. Phys. Commun., 2025)