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

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

(2015) Chad W. Hopkins et al.   Journal of Chemical Theory and Computation

Reversible and Irreversible Adsorption Energetics of Poly(ethylene glycol) and Sorbitan Poly(ethoxylate) at a Water/Alkane Interface

(2015) Kyle J. Huston et al.   LANGMUIR

Detecting vapour bubbles in simulations of metastable water

(2014) Miguel A. González et al.   JOURNAL OF CHEMICAL PHYSICS

Proton Ordering of Cubic Ice Ic: Spectroscopy and Computer Simulations

(2014) Philipp Geiger et al.   Journal of Physical Chemistry C

Metastable liquid–liquid transition in a molecular model of water

(2014) Jeremy C. Palmer et al.   NATURE

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

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

Conservative integration of rigid body motion by quaternion parameters with implicit constraints

(2012) M.B. Nielsen et al.   INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING

Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water

(2012) Aleks Reinhardt et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamical cage behaviour and hydrogen migration in hydrogen and hydrogen-tetrahydrofuran clathrate hydrates

(2012) Paul D. Gorman et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2012) Christopher Knorowski et al.   Soft Matter

Molecular dynamics simulations of vapor/liquid coexistence using the nonpolarizable water models

(2011) Ryuji Sakamaki et al.   JOURNAL OF CHEMICAL PHYSICS

Communication: Shifted forces in molecular dynamics

(2011) Søren Toxvaerd et al.   JOURNAL OF CHEMICAL PHYSICS

Equipartition and the Calculation of Temperature in Biomolecular Simulations

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

Rigid-Body Molecular Dynamics of Fullerene-Based Nanocars on Metallic Surfaces

(2010) Sergei S. Konyukhov 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

Hybrid Monte Carlo Simulations Combined with a Phase Mixture Model to Predict the Structural Transitions of a Porous Metal−Organic Framework Material upon Adsorption of Guest Molecules

(2010) A. Ghoufi et al.   Journal of Physical Chemistry C

A theoretical examination of known and hypothetical clathrate hydrate materials

(2009) Gareth A. Tribello et al.   JOURNAL OF CHEMICAL PHYSICS

General formulation of pressure and stress tensor for arbitrary many-body interaction potentials under periodic boundary conditions

(2009) Aidan P. Thompson et al.   JOURNAL OF CHEMICAL PHYSICS

Anisotropic self-assembly of spherical polymer-grafted nanoparticles

(2009) Pinar Akcora et al.   NATURE MATERIALS

EFFICIENT NUMERICAL DIAGONALIZATION OF HERMITIAN 3 × 3 MATRICES

(2008) JOACHIM KOPP   INTERNATIONAL JOURNAL OF MODERN PHYSICS C

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

Molecular Dynamics of Surface-Moving Thermally Driven Nanocars

(2008) Alexei V. Akimov et al.   Journal of Chemical Theory and Computation

Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats

(2008) Amit Mor et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Processed splitting algorithms for rigid-body molecular dynamics simulations

(2008) Igor P. Omelyan   PHYSICAL REVIEW E

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