Refinement of thermostated molecular dynamics using backward error analysis

Comment on “The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water” [I and II: J. Chem. Phys. 135, 134503 (2011); J. Chem. Phys. 138, 214504 (2013)]

(2018) Jeremy C. Palmer et al.   JOURNAL OF CHEMICAL PHYSICS

Anomalous Effects of Velocity Rescaling Algorithms: The Flying Ice Cube Effect Revisited

(2018) Efrem Braun et al.   Journal of Chemical Theory and Computation

Molecular dynamics with rigid bodies: Alternative formulation and assessment of its limitations when employed to simulate liquid water

(2017) Ana J. Silveira et al.   JOURNAL OF CHEMICAL PHYSICS

New Langevin and gradient thermostats for rigid body dynamics

(2015) R. L. Davidchack et al.   JOURNAL OF CHEMICAL PHYSICS

Force field comparison and thermodynamic property calculation of supercritical CO2 and CH4 using molecular dynamics simulations

(2014) Cassiano G. Aimoli et al.   FLUID PHASE EQUILIBRIA

Transport properties of carbon dioxide and methane from molecular dynamics simulations

(2014) C. G. Aimoli et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-grain molecular dynamics simulations of nanoparticle-polymer melt: Dispersion vs. agglomeration

(2013) Tarak K. Patra et al.   JOURNAL OF CHEMICAL PHYSICS

Neural networks for local structure detection in polymorphic systems

(2013) Philipp Geiger et al.   JOURNAL OF CHEMICAL PHYSICS

The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water. II

(2013) David T. Limmer et al.   JOURNAL OF CHEMICAL PHYSICS

Polymer directed aggregation and dispersion of anisotropic nanoparticles

(2013) Tarak K. Patra et al.   Soft Matter

Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles

(2012) Michael R. Shirts   Journal of Chemical Theory and Computation

Charge Transfer and Chemisorption of Fullerene Molecules on Metal Surfaces: Application to Dynamics of Nanocars

(2012) Alexey V. Akimov et al.   Journal of Physical Chemistry C

Porous Carbon Nanotube Membranes for Separation of H2/CH4 and CO2/CH4 Mixtures

(2012) Benjamin J. Bucior et al.   Journal of Physical Chemistry C

Dynamics of DNA-programmable nanoparticle crystallization: gelation, nucleation and topological defects

(2012) Christopher Knorowski et al.   Soft Matter

The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water

(2011) David T. Limmer et al.   JOURNAL OF CHEMICAL PHYSICS

Batch means and spectral variance estimators in Markov chain Monte Carlo

(2010) James M. Flegal et al.   ANNALS OF STATISTICS

Equipartition and the Calculation of Temperature in Biomolecular Simulations

(2010) Michael P. Eastwood et al.   Journal of Chemical Theory and Computation

Discretization errors in molecular dynamics simulations with deterministic and stochastic thermostats

(2010) Ruslan L. Davidchack   JOURNAL OF COMPUTATIONAL PHYSICS

Langevin thermostat for rigid body dynamics

(2009) Ruslan L. Davidchack et al.   JOURNAL OF CHEMICAL PHYSICS

A Gentle Stochastic Thermostat for Molecular Dynamics

(2009) Ben Leimkuhler et al.   JOURNAL OF STATISTICAL PHYSICS

Efficient algorithms for rigid body integration using optimized splitting methods and exact free rotational motion

(2008) Ramses van Zon et al.   JOURNAL OF CHEMICAL PHYSICS

On the generalized equipartition theorem in molecular dynamics ensembles and the microcanonical thermodynamics of small systems

(2008) Mark J. Uline et al.   JOURNAL OF CHEMICAL PHYSICS

General purpose molecular dynamics simulations fully implemented on graphics processing units

(2008) Joshua A. Anderson et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Processed splitting algorithms for rigid-body molecular dynamics simulations

(2008) Igor P. Omelyan   PHYSICAL REVIEW E

Self-Assembled Chiral Superstructures Composed of Rigid Achiral Molecules and Molecular Scale Chiral Induction by Dopants

(2008) Fangyong Yan et al.   PHYSICAL REVIEW LETTERS

The Exact Computation of the Free Rigid Body Motion and Its Use in Splitting Methods

(2008) E. Celledoni et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING