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Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations.Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures.Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.Introducing sampling entropy in repository based adaptive umbrella sampling.Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.Error and efficiency of simulated tempering simulations.Generalized simulated tempering for exploring strong phase transitions.Simulated tempering yields insight into the low-resolution Rosetta scoring functions.The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systemsAccelerating the weighted histogram analysis method by direct inversion in the iterative subspace.Collective variable approaches for single molecule flexible fitting and enhanced sampling.Comparison of sampling efficiency between simulated tempering and replica exchange.Communication: Multiple atomistic force fields in a single enhanced sampling simulation.Communication: Simulated tempering with fast on-the-fly weight determination.Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing.Quenching protein dynamics interferes with HIV capsid maturation.RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Optimal updating magnitude in adaptive flat-distribution sampling.A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs.Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states.On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics.Simulations in generalized ensembles through noninstantaneous switches.Comparing parallel- and simulated-tempering-enhanced sampling algorithms at phase-transition regimes.A simple protocol for the probability weights of the simulated tempering algorithm: applications to first-order phase transitions.Comparison of the serial and parallel algorithms of generalized ensemble simulations: an analytical approach.Estimating thermodynamic expectations and free energies in expanded ensemble simulations: Systematic variance reduction through conditioning.Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
P2860
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P2860
description
2007 nî lūn-bûn
@nan
2007年の論文
@ja
2007年学术文章
@wuu
2007年学术文章
@zh
2007年学术文章
@zh-cn
2007年学术文章
@zh-hans
2007年学术文章
@zh-my
2007年学术文章
@zh-sg
2007年學術文章
@yue
2007年學術文章
@zh-hant
name
Choosing weights for simulated tempering.
@en
Choosing weights for simulated tempering.
@nl
type
label
Choosing weights for simulated tempering.
@en
Choosing weights for simulated tempering.
@nl
prefLabel
Choosing weights for simulated tempering.
@en
Choosing weights for simulated tempering.
@nl
P2860
P1433
P1476
Choosing weights for simulated tempering.
@en
P2093
Sanghyun Park
Vijay S Pande
P2860
P304
P356
10.1103/PHYSREVE.76.016703
P407
P433
P577
2007-07-16T00:00:00Z