scholarly journals Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface

2008 ◽  
Vol 128 (3) ◽  
pp. 034105 ◽  
Author(s):  
Hao Hu ◽  
Zhenyu Lu ◽  
Jerry M. Parks ◽  
Steven K. Burger ◽  
Weitao Yang
Keyword(s):  
Free Energy ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Sequential Sampling ◽  
Minimum Free Energy ◽  
Potential Of Mean Force

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 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

scholarly journals Thermodynamic and Kinetic Characterization of Protein Conformational Dynamics within a Riemannian Framework

2021 ◽  
Author(s):  
Curtis Goolsby ◽  
Ashkan Fakharzadeh ◽  
Mahmoud Moradi
Keyword(s):  
Free Energy ◽  
Transition Rate ◽  
Conformational Dynamics ◽  
Diffusion Constant ◽  
Minimum Free Energy ◽  
Umbrella Sampling ◽  
Potential Of Mean Force ◽  
Collective Variable ◽  
Bayesian Estimator ◽  
Riemannian Framework

AbstractWe have formulated a Riemannian framework for describing the geometry of collective variable spaces of biomolecules within the context of molecular dynamics (MD) simulations. The formalism provides a theoretical framework to develop enhanced sampling techniques, path-finding algorithms, and transition rate estimators consistent with a Riemannian treatment of the collective variable space, where the quantities of interest such as the potential of mean force (PMF) and minimum free energy path (MFEP) remain invariant under coordinate transformation. Specific algorithms within this framework are discussed such as the Riemannian umbrella sampling, the Riemannian string method, and a Riemannian-Bayesian estimator of free energy and diffusion constant, which can be used to estimate the transition rate along an MFEP.

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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