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Polymorphic transitions in single crystals: A new molecular dynamics method
A new Lagrangian formulation is introduced. It can be used to make molecular dynamics (MD) calculations on systems under the most general, externally applied, conditions of stress. In this…
Canonical sampling through velocity rescaling.
The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution and can be used to measure the accuracy of the sampling.
Escaping free-energy minima
We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the…
Generalized neural-network representation of high-dimensional potential-energy surfaces.
A new kind of neural-network representation of DFT potential-energy surfaces is introduced, which provides the energy and forces as a function of all atomic positions in systems of arbitrary size and is several orders of magnitude faster than DFT.
Well-tempered metadynamics: a smoothly converging and tunable free-energy method.
We present a method for determining the free-energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics…
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
Crystal structure and pair potentials: A molecular-dynamics study
With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different…
Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach
The nature of the hydrated excess proton in water
Explanations for the anomalously high mobility of protons in liquid water began with Grotthuss's idea, of ‘structural diffusion’ nearly two centuries ago. Subsequent explanations have refined this…
From A to B in free energy space.
A new method for searching low free energy paths in complex molecular systems at finite temperature is presented that combines features of approaches such as metadynamics or umbrella sampling with those of path based methods and introduces two variables that are able to describe the position of a point in configuration space relative to a preassigned path.