Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes
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Recent advances in QM/MM free energy calculations using reference potentialsConstant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian ExchangeMolecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based modelsPredicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulationsMultiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.Computational scheme for pH-dependent binding free energy calculation with explicit solvent.QM/MM free energy simulations: recent progress and challengesPerspective: Quantum mechanical methods in biochemistry and biophysics.Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method.An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.Applications of quantum mechanical/molecular mechanical methods to the chemical insertion step of DNA and RNA polymerization.Quantum mechanical force fields for condensed phase molecular simulations.Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.Partition coefficients for the SAMPL5 challenge using transfer free energies.An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulationsSolvation free energies for periodic surfaces: comparison of implicit and explicit solvation models.Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities.Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections.Introducing the mean field approximation to CDFT/MMpol method: Statistically converged equilibrium and nonequilibrium free energy calculation for electron transfer reactions in condensed phases.BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation.Mechanism and reactivity in the Morita-Baylis-Hillman reaction: the challenge of accurate computations.Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challengeConvergence of single-step free energy perturbation
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Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes
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article científic
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article scientifique
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articolo scientifico
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artigo científico
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bilimsel makale
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scientific article published on 11 February 2014
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vedecký článok
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vetenskaplig artikel
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videnskabelig artikel
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vědecký článek
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name
Multiscale Free Energy Simulat ...... nn Bennett Reweighting Schemes
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Multiscale Free Energy Simulat ...... n Bennett Reweighting Schemes.
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type
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Multiscale Free Energy Simulat ...... nn Bennett Reweighting Schemes
@en
Multiscale Free Energy Simulat ...... n Bennett Reweighting Schemes.
@nl
prefLabel
Multiscale Free Energy Simulat ...... nn Bennett Reweighting Schemes
@en
Multiscale Free Energy Simulat ...... n Bennett Reweighting Schemes.
@nl
P2860
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P1476
Multiscale Free Energy Simulat ...... nn Bennett Reweighting Schemes
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P2093
H Lee Woodcock
P2860
P304
P356
10.1021/CT401118K
P577
2014-02-11T00:00:00Z