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A mixed alchemical and equilibrium dynamics to simulate heterogeneous dense fluids: Illustrations for Lennard-Jones mixtures and phospholipid membranes
A novel density functional theory for atoms, molecules, and solids
Bond selective dissociation of methane (CH3D) on the steps and terraces of Pt(211)
Atomistic and mesoscale simulation of sodium and potassium adsorption in cement paste
SPECIAL TOPIC: ENHANCED SAMPLING FOR MOLECULAR SYSTEMS
Preface
Preface: Special Topic on Enhanced Sampling for Molecular Systems
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072001 (2018)
https://doi.org/10.1063/1.5049669
Articles
Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072301 (2018)
https://doi.org/10.1063/1.5025487
Adaptive landscape flattening in amino acid sequence space for the computational design of protein:peptide binding
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072302 (2018)
https://doi.org/10.1063/1.5022249
Forward-flux sampling with jumpy order parameters
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072303 (2018)
https://doi.org/10.1063/1.5018303
Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072304 (2018)
https://doi.org/10.1063/1.5016222
Chemical potential calculations in non-homogeneous liquids
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072305 (2018)
https://doi.org/10.1063/1.5024631
Efficient sampling of puckering states of monosaccharides through replica exchange with solute tempering and bond softening
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072306 (2018)
https://doi.org/10.1063/1.5024389
Prediction of the phase equilibria for island-type asphaltenes via HMC-WL simulations
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072307 (2018)
https://doi.org/10.1063/1.5023810
Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072308 (2018)
https://doi.org/10.1063/1.5024217
Frequency adaptive metadynamics for the calculation of rare-event kinetics
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072309 (2018)
https://doi.org/10.1063/1.5024679
Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072310 (2018)
https://doi.org/10.1063/1.5027004
Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072311 (2018)
https://doi.org/10.1063/1.5027439
Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072312 (2018)
https://doi.org/10.1063/1.5023804
Temperature-induced collapse of a disordered peptide observed by three sampling methods in molecular dynamics simulations
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072313 (2018)
https://doi.org/10.1063/1.5027409
Multiscale enhanced sampling of glucokinase: Regulation of the enzymatic reaction via a large scale domain motion
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072314 (2018)
https://doi.org/10.1063/1.5027444
A generalized linear response framework for expanded ensemble and replica exchange simulations
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072315 (2018)
https://doi.org/10.1063/1.5027494
Endpoint-restricted adiabatic free energy dynamics approach for the exploration of biomolecular conformational equilibria
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072316 (2018)
https://doi.org/10.1063/1.5027479
Folding free energy landscapes of β-sheets with non-polarizable and polarizable CHARMM force fields
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072317 (2018)
https://doi.org/10.1063/1.5025951
Molecular exchange Monte Carlo: A generalized method for identity exchanges in grand canonical Monte Carlo simulations
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072318 (2018)
https://doi.org/10.1063/1.5025184
Improving low-accuracy protein structures using enhanced sampling techniques
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072319 (2018)
https://doi.org/10.1063/1.5027243
Advances in enhanced sampling along adaptive paths of collective variables
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072320 (2018)
https://doi.org/10.1063/1.5027392
Reservoir pH replica exchange
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072321 (2018)
https://doi.org/10.1063/1.5027413
Development of a generalized hybrid Monte Carlo algorithm to generate the multicanonical ensemble with applications to molecular systems
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072322 (2018)
https://doi.org/10.1063/1.5028466
Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072323 (2018)
https://doi.org/10.1063/1.5027580
Limiting relaxation times from Markov state models
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072324 (2018)
https://doi.org/10.1063/1.5027203
A mixed alchemical and equilibrium dynamics to simulate heterogeneous dense fluids: Illustrations for Lennard-Jones mixtures and phospholipid membranes
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072325 (2018)
https://doi.org/10.1063/1.5027078
Layered nested Markov chain Monte Carlo
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072326 (2018)
https://doi.org/10.1063/1.5030531
Heterogeneous seeded molecular dynamics as a tool to probe the ice nucleating ability of crystalline surfaces
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072327 (2018)
https://doi.org/10.1063/1.5029336
Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072328 (2018)
https://doi.org/10.1063/1.5027100
Exploring potential crossing seams in periodic systems: Intersystem crossing pathways in the benzene crystal
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072329 (2018)
https://doi.org/10.1063/1.5025023
Investigating the role of non-covalent interactions in conformation and assembly of triazine-based sequence-defined polymers
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072330 (2018)
https://doi.org/10.1063/1.5024552
Understanding the unique sorption of alkane-α, ω-diols in silicalite-1
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072331 (2018)
https://doi.org/10.1063/1.5026937
Glassy dynamics in mutant huntingtin proteins
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072333 (2018)
https://doi.org/10.1063/1.5029369
Isomerization kinetics of flexible molecules in the gas phase: Atomistic versus coarse-grained sampling
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072334 (2018)
https://doi.org/10.1063/1.5026688
Girsanov reweighting for metadynamics simulations
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072335 (2018)
https://doi.org/10.1063/1.5027728
Transition path theory from biased simulations
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072336 (2018)
https://doi.org/10.1063/1.5027253
An efficient Bayesian kinetic lumping algorithm to identify metastable conformational states via Gibbs sampling
In Special Collection:
Enhanced Sampling for Molecular Systems
J. Chem. Phys. 149, 072337 (2018)
https://doi.org/10.1063/1.5027001
Redox potential replica exchange molecular dynamics at constant pH in AMBER: Implementation and validation
J. Chem. Phys. 149, 072338 (2018)
https://doi.org/10.1063/1.5027379
ARTICLES
Theoretical Methods and Algorithms
Structural, electronic, vibrational, and superconducting properties of hydrogenated chlorine
J. Chem. Phys. 149, 074101 (2018)
https://doi.org/10.1063/1.5031202
Dynamic bounds on stochastic chemical kinetic systems using semidefinite programming
J. Chem. Phys. 149, 074103 (2018)
https://doi.org/10.1063/1.5029926
A novel density functional theory for atoms, molecules, and solids
J. Chem. Phys. 149, 074104 (2018)
https://doi.org/10.1063/1.5038262
Atoms, Molecules, and Clusters
Pervasive interactions between methyl torsion and low frequency vibrations in S and S1 p-fluorotoluene
J. Chem. Phys. 149, 074301 (2018)
https://doi.org/10.1063/1.5035461
Electronic bands of scandium monocarbide, ScC, in the region 14 140–16 000 cm−1
J. Chem. Phys. 149, 074302 (2018)
https://doi.org/10.1063/1.5044236
Correlation of structure with UV-visible spectra by varying SH composition in Au-SH nanoclusters
J. Chem. Phys. 149, 074307 (2018)
https://doi.org/10.1063/1.5031478
Liquids, Glasses, and Crystals
Comparison of single particle dynamics at the center and on the surface of equilibrium glassy films
J. Chem. Phys. 149, 074501 (2018)
https://doi.org/10.1063/1.5039505
Nanometer scale thermal response of polymers to fast thermal perturbations
J. Chem. Phys. 149, 074503 (2018)
https://doi.org/10.1063/1.5044187
Second virial coefficient properties of the n-m Lennard-Jones/Mie potential
J. Chem. Phys. 149, 074504 (2018)
https://doi.org/10.1063/1.5041320
Polyamorphism and liquid-liquid transformations in D-mannitol
J. Chem. Phys. 149, 074505 (2018)
https://doi.org/10.1063/1.5041757
Surfaces, Interfaces, and Materials
Bond selective dissociation of methane (CH3D) on the steps and terraces of Pt(211)
In Special Collection:
JCP Editors' Choice 2018
J. Chem. Phys. 149, 074701 (2018)
https://doi.org/10.1063/1.5041349
Structural and dynamic properties of water molecules in a uniformly charged nanopore
J. Chem. Phys. 149, 074703 (2018)
https://doi.org/10.1063/1.5042107
Atomistic and mesoscale simulation of sodium and potassium adsorption in cement paste
J. Chem. Phys. 149, 074705 (2018)
https://doi.org/10.1063/1.5042755
Polymers and Soft Matter
Dynamical structure of entangled polymers simulated under shear flow
J. Chem. Phys. 149, 074901 (2018)
https://doi.org/10.1063/1.5035170
Nanoscale cavitation in perforation of cellular membrane by shock-wave induced nanobubble collapse
J. Chem. Phys. 149, 074902 (2018)
https://doi.org/10.1063/1.5037643
