Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study.
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A kinetic model of trp-cage folding from multiple biased molecular dynamics simulationsLarge-scale conformational changes of Trypanosoma cruzi proline racemase predicted by accelerated molecular dynamics simulationFunctional loop dynamics of the streptavidin-biotin complexIntroducing sampling entropy in repository based adaptive umbrella sampling.Cross dimerization of amyloid-β and αsynuclein proteins in aqueous environment: a molecular dynamics simulations study.Studying functional dynamics in bio-molecules using accelerated molecular dynamics.Implementation of Accelerated Molecular Dynamics in NAMDEnhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics.Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations.w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped ConformationsUnconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A ReviewE9-Im9 colicin DNase-immunity protein biomolecular association in water: a multiple-copy and accelerated molecular dynamics simulation studyFree energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamicsSubstrate-dependent dynamics of UDP-galactopyranose mutase: Implications for drug design.Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics.Trypsinogen activation as observed in accelerated molecular dynamics simulations.Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates.Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol.A new class of enhanced kinetic sampling methods for building Markov state models.Gaussian Accelerated Molecular Dynamics in NAMD.Optimized Markov state models for metastable systems.Dynamic properties of force fields.Non-Boltzmann sampling and Bennett's acceptance ratio method: how to profit from bending the rules.Uncertainty in a Markov state model with missing states and rates: Application to a room temperature kinetic model obtained using high temperature molecular dynamics.Integrating diffusion maps with umbrella sampling: application to alanine dipeptide.Practical hyperdynamics method for systems with large changes in potential energy.
P2860
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P2860
Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study.
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name
Estimating kinetic rates from ...... licit solvent as a case study.
@en
Estimating kinetic rates from ...... licit solvent as a case study.
@nl
type
label
Estimating kinetic rates from ...... licit solvent as a case study.
@en
Estimating kinetic rates from ...... licit solvent as a case study.
@nl
prefLabel
Estimating kinetic rates from ...... licit solvent as a case study.
@en
Estimating kinetic rates from ...... licit solvent as a case study.
@nl
P2860
P356
P1476
Estimating kinetic rates from ...... licit solvent as a case study.
@en
P2093
César Augusto F de Oliveira
Donald Hamelberg
P2860
P304
P356
10.1063/1.2794763
P407
P577
2007-11-01T00:00:00Z