Browsing by Author "Barrozo, Alexandre"

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    Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations
    (ELSEVIER, 2018-01-04) Bauer, Paul; Barrozo, Alexandre; Purg, Miha; Amrein, Beat Anton; Esguerra, Mauricio; Wilson, Philippe B.; Major, Dan Thomas; Aqvist, Johan; Kamerlin, Shina Caroline Lynn
    Atomistic simulations have become one of the main approaches to study the chemistry and dynamics of biomolecular systems in solution. Chemical modelling is a powerful way to understand biochemistry, with a number of different programs available to perform specialized calculations. We present here Q6, a new version of the Q software package, which is a generalized package for empirical valence bond, linear interaction energy, and other free energy calculations. In addition to general technical improvements, Q6 extends the reach of the EVB implementation to fast approximations of quantum effects, extended solvent descriptions and quick estimation of the contributions of individual residues to changes in the activation free energy of reactions.