Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer

2016 ◽  
Vol 7 (21) ◽  
pp. 4391-4397 ◽  
Author(s):  
Jesús I. Mendieta-Moreno ◽  
Daniel G. Trabada ◽  
Jesús Mendieta ◽  
James P. Lewis ◽  
Paulino Gómez-Puertas ◽  
...  
Keyword(s):  
Free Energy ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Photochemical Reaction ◽  
Thymine Dimer ◽  
Energy Maps ◽  
Cyclobutane Thymine Dimer

Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics

2016 ◽  
Vol 12 (2) ◽  
pp. 499-511 ◽  
Author(s):  
Xiangyu Jia ◽  
Meiting Wang ◽  
Yihan Shao ◽  
Gerhard König ◽  
Bernard R. Brooks ◽  
...  
Keyword(s):  
Free Energy ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Solvation Free Energy

Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation

2013 ◽  
Vol 139 (6) ◽  
pp. 064105 ◽  
Author(s):  
Iakov Polyak ◽  
Tobias Benighaus ◽  
Eliot Boulanger ◽  
Walter Thiel
Keyword(s):  
Free Energy ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Free Energy Perturbation ◽  
Energy Perturbation

BAR-based multi-dimensional nonequilibrium pulling for indirect construction of QM/MM free energy landscapes: from semi-empirical to ab initio

2019 ◽  
Vol 21 (39) ◽  
pp. 21942-21959 ◽  
Author(s):  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Quantum Mechanics ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Indirect Method ◽  
Energy Landscapes ◽  
Free Energy Landscapes ◽  
Energy Simulations ◽  
Semi Empirical

The indirect method for the construction of quantum mechanics (QM)/molecular mechanics (MM) free energy landscapes provides a cheaper alternative for free energy simulations at the QM level.

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