Michele Parrinello

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 formulation the MD cell shape and size can change according to dynamical equations given by this Lagrangian. This new MD technique is well suited to the study of structural transformations in solids under external stress and at finite temperature. As an example of the use of this technique we show how a single crystal of Ni behaves under uniform uniaxial compressive and tensile loads. This work confirms some of the results of static (i.e., zero temperature) calculations reported in the literature. We also show that some results regarding the stress‐strain relation obtained by static calculations are invalid at finite temperature. We find that, under compressive loading, our model of Ni shows a bifurcation in its stress‐strain relation; this bifurcation provides a link in configuration space between cubic and hexagonal c...

Canonical sampling through velocity rescaling

The authors present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. 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. In numerical applications this quantity can be used to measure the accuracy of the sampling. The authors illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent of the thermostat parameter also with regard to the dynamic properties.

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 space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the FES, allowing the efficient exploration and accurate determination of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.

Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach

Abstract We present the Gaussian and plane waves (GPW) method and its implementation in Quickstep which is part of the freely available program package CP2K. The GPW method allows for accurate density functional calculations in gas and condensed phases and can be effectively used for molecular dynamics simulations. We show how derivatives of the GPW energy functional, namely ionic forces and the Kohn–Sham matrix, can be computed in a consistent way. The computational cost of computing the total energy and the Kohn–Sham matrix is scaling linearly with the system size, even for condensed phase systems of just a few tens of atoms. The efficiency of the method allows for the use of large Gaussian basis sets for systems up to 3000 atoms, and we illustrate the accuracy of the method for various basis sets in gas and condensed phases. Agreement with basis set free calculations for single molecules and plane wave based calculations in the condensed phase is excellent. Wave function optimisation with the orbital transformation technique leads to good parallel performance, and outperforms traditional diagonalisation methods. Energy conserving Born–Oppenheimer dynamics can be performed, and a highly efficient scheme is obtained using an extrapolation of the density matrix. We illustrate these findings with calculations using commodity PCs as well as supercomputers.

The nature of the hydrated excess proton in water

Explanations for the anomalously high mobility of protons in liquid water began with Grotthusss idea, of ‘structural diffusion’ nearly two centuries ago. Subsequent explanations have refined this concept by invoking thermal hopping, , proton tunnelling, or solvation effects. More recently, two main structural models have emerged for the hydrated proton. Eigen, proposed the formation of an H9O4+ complex in which an H3O+ core is strongly hydrogen-bonded to three H2O molecules. Zundel, , meanwhile, supported the notion of an H5O2+ complex in which the proton isshared between two H2O molecules. Here we use ab initio path integral simulations to address this question. These simulations include time-independent equilibrium thermal and quantum fluctuations of all nuclei, and determine interatomic interactions from the electronic structure. We find that the hydrated proton forms a fluxional defect in the hydrogen-bonded network, with both H9O4+ and H5O2+ occurring only in thesense of ‘limiting’ or ‘ideal’ structures. The defect can become delocalized over several hydrogen bonds owing to quantum fluctuations. Solvent polarization induces a small barrier to proton transfer, which is washed out by zero-point motion. The proton can consequently be considered part of a ‘low-barrier hydrogen bond’, , in which tunnelling is negligible and the simplest concepts of transition-state theory do not apply. The rate of proton diffusion is determined by thermally induced hydrogen-bond breaking in the second solvation shell.

PLUMED: a portable plugin for free-energy calculations with molecular dynamics

Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both Fortran and C/C++ codes.

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 and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only on the physically relevant regions of the order parameter space. The algorithm is tested on the reconstruction of an alanine dipeptide free-energy landscape.

A hybrid Gaussian and plane wave density functional scheme

A density functional theory-based algorithm for periodic and non-periodic ab initio calculations is presented. This scheme uses pseudopotentials in order to integrate out the core electrons from the problem. The valence pseudo-wavefunctions are expanded in Gaussian-type orbitals and the density is represented in a plane wave auxiliary basis. The Gaussian basis functions make it possible to use the efficient analytical integration schemes and screening algorithms of quantum chemistry. Novel recursion relations are developed for the calculation of the matrix elements of the density-dependent Kohn-Sham self-consistent potential. At the same time the use of a plane wave basis for the electron density permits efficient calculation of the Hartree energy using fast Fourier transforms, thus circumventing one of the major bottlenecks of standard Gaussian based calculations. Furthermore, this algorithm avoids the fitting procedures that go along with intermediate basis sets for the charge density. The performance a...

The nature and transport mechanism of hydrated hydroxide ions in aqueous solution

Compared to other ions, protons (H+) and hydroxide ions (OH-) exhibit anomalously high mobilities in aqueous solutions. On a qualitative level, this behaviour has long been explained by ‘structural diffusion’—the continuous interconversion between hydration complexes driven by fluctuations in the solvation shell of the hydrated ions. Detailed investigations have led to a clear understanding of the proton transport mechanism at the molecular level. In contrast, hydroxide ion mobility in basic solutions has received far less attention, even though bases and base catalysis play important roles in many organic and biochemical reactions and in the chemical industry. The reason for this may be attributed to the century-old notion that a hydrated OH- can be regarded as a water molecule missing a proton, and that the transport mechanism of such a ‘proton hole’ can be inferred from that of an excess proton by simply reversing hydrogen bond polarities. However, recent studies have identified OH- hydration complexes that bear little structural similarity to proton hydration complexes. Here we report the solution structures and transport mechanisms of hydrated hydroxide, which we obtained from first-principles computer simulations that explicitly treat quantum and thermal fluctuations of all nuclei. We find that the transport mechanism, which differs significantly from the proton hole picture, involves an interplay between the previously identified hydration complexes and is strongly influenced by nuclear quantum effects.

Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water

Charge defects in water created by excess or missing protons appear in the form of solvated hydronium H3O+ and hydroxyl OH− ions. Using the method of ab initio molecular dynamics, we have investigated the structure and proton transfer dynamics of the solvation complexes, which embed the ions in the network of hydrogen bonds in the liquid. In our ab initio molecular dynamics approach, the interatomic forces are calculated each time step from the instantaneous electronic structure using density functional methods. All hydrogen atoms, including the excess proton, are treated as classical particles with the mass of a deuterium atom. For the H3O+ ion we find a dynamic solvation complex, which continuously fluctuates between a (H5O2)+ and a (H9O4)+ structure as a result of proton transfer. The OH− has a predominantly planar fourfold coordination forming a (H9O5)− complex. Occasionally this complex is transformed in a more open tetrahedral (H7O4)− structure. Proton transfer is observed only for the more waterlik...