Biased sampling of nonequilibrium trajectories: can fast switching simulations outperform conventional free energy calculation methods?
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Velocity convergence of free energy surfaces from single-molecule measurements using Jarzynski's equality.Density-dependent analysis of nonequilibrium paths improves free energy estimatesLooking for some free energy? Call JEFREE (…).Structure-Based, Rational Design of T Cell Receptors.Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.Replica exchange with nonequilibrium switches.Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages.Protein-protein interaction investigated by steered molecular dynamics: the TCR-pMHC complex.Waste-recycling Monte Carlo with optimal estimates: application to free energy calculations in alloys.Work distribution for the adiabatic compression of a dilute and interacting classical gas.Parallel-pulling protocol for free-energy evaluation.Nonequilibrium work energy relation for non-Hamiltonian dynamics.Application of principal component analysis in protein unfolding: an all-atom molecular dynamics simulation study.I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework.Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures.Impact of interfacial high-density water layer on accurate estimation of adsorption free energy by Jarzynski's equality.Preserving correlations between trajectories for efficient path sampling.Towards bulk thermodynamics via non-equilibrium methods: gaseous methane as a case study.Probing the conformational energetics of alkyl thiols on gold surfaces by means of a morphing/steering non-equilibrium tool.High-precision work distributions for extreme nonequilibrium processes in large systems.Stochastic thermodynamics of fluctuating density fields: non-equilibrium free energy differences under coarse-graining.Force-clamp experiments reveal the free-energy profile and diffusion coefficient of the collapse of protein molecules.Average entropy dissipation in irreversible mesoscopic processes.Density-dependent analysis of nonequilibrium paths improves free energy estimates II. A Feynman-Kac formalism.Optimum protocol for fast-switching free-energy calculations.Nonequilibrium fluctuation theorems in the presence of a time-reversal symmetry-breaking field and nonconservative forces.Application range of Jarzynski's equation for boundary-switching processes.Entropy-energy decomposition from nonequilibrium work trajectories.Single molecule pulling with large time steps.A proof of Jarzynski's nonequilibrium work theorem for dynamical systems that conserve the canonical distribution.Equilibrium free energies from fast-switching trajectories with large time steps.Escorted free energy simulations: improving convergence by reducing dissipation.Computing Equilibrium Free Energies Using Non-Equilibrium Molecular DynamicsEquilibrium Free Energies from Nonequilibrium Metadynamics
P2860
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P2860
Biased sampling of nonequilibrium trajectories: can fast switching simulations outperform conventional free energy calculation methods?
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2005 nî lūn-bûn
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2005年の論文
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2005年学术文章
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2005年学术文章
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name
Biased sampling of nonequilibr ...... ee energy calculation methods?
@en
Biased sampling of nonequilibr ...... ee energy calculation methods?
@nl
type
label
Biased sampling of nonequilibr ...... ee energy calculation methods?
@en
Biased sampling of nonequilibr ...... ee energy calculation methods?
@nl
prefLabel
Biased sampling of nonequilibr ...... ee energy calculation methods?
@en
Biased sampling of nonequilibr ...... ee energy calculation methods?
@nl
P356
P1476
Biased sampling of nonequilibr ...... ee energy calculation methods?
@en
P2093
Christoph Dellago
Phillip L Geissler
P304
P356
10.1021/JP044556A
P407
P577
2005-04-01T00:00:00Z