TY - JOUR
T1 - Q6
T2 - A comprehensive toolkit for empirical valence bond and related free energy calculations
AU - Bauer, Paul
AU - Barrozo, Alexandre
AU - Purg, Miha
AU - Amrein, Beat Anton
AU - Esguerra, Mauricio
AU - Wilson, Philippe Barrie
AU - Major, Dan Thomas
AU - Åqvist, Johan
AU - Kamerlin, Shina Caroline Lynn
N1 - Publisher Copyright:
© 2017
PY - 2018/1/1
Y1 - 2018/1/1
N2 - 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.
AB - 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.
KW - Empirical valence bond
KW - Free energy perturbation
KW - Molecular dynamics simulations
KW - Path integral calculations
UR - http://www.scopus.com/inward/record.url?scp=85039924956&partnerID=8YFLogxK
U2 - 10.1016/j.softx.2017.12.001
DO - 10.1016/j.softx.2017.12.001
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SN - 2352-7110
VL - 7
SP - 388
EP - 395
JO - SoftwareX
JF - SoftwareX
ER -