arXiv subjects

M. Parrinello

Publications and source records attributed to M. Parrinello.

11 recordsLinked to original sources

arXiv2010

Enhanced Sampling in the Well-Tempered Ensemble

We introduce the well-tempered ensemble (WTE) which is the biased ensemble sampled by well-tempered metadynamics when the energy is used as collective variable. WTE can be designed so as to have approximately the same average energy as the canonical ensemble but much larger fluctuations. These two properties lead to an extremely fast exploration of phase space. An even greater efficiency is obtained when WTE is combined with parallel tempering. Unbiased Boltzmann averages are computed on the fly by a recently developed reweighting method [M. Bonomi et al. J. Comput. Chem. 30, 1615 (2009)]. We apply WTE and its parallel tempering variant to the 2d Ising model and to a Go-model of HIV protease, demonstrating in these two representative cases that convergence is accelerated by orders of magnitude.

cond-mat.stat-mech↗

arXiv2009

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.

physics.comp-ph↗

arXiv2008

Coexistence of tetrahedral and octahedral-like sites in amorphous phase change materials

Chalcogenide alloys are materials of interest for optical recording and non-volatile memories. We perform ab-initio molecular dynamics simulations aiming at shading light onto the structure of amorphous Ge2Sb2Te5 (GST), the prototypical material in this class. First principles simulations show that amorphous GST obtained by quenching from the liquid phase displays two types of short range order. One third of Ge atoms are in a tetrahedral environment while the remaining Ge, Sb and Te atoms display a defective octahedral environment, reminiscent of cubic crystalline GST.

cond-mat.mtrl-sci↗

arXiv2005

Evolution of the structure of amorphous ice - from low-density amorphous (LDA) through high-density amorphous (HDA) to very high-density amorphous (VHDA) ice

We report results of molecular dynamics simulations of amorphous ice for pressures up to 22.5 kbar. The high-density amorphous ice (HDA) as prepared by pressure-induced amorphization of Ih ice at T=80 K is annealed to T=170 K at various pressures to allow for relaxation. Upon increase of pressure, relaxed amorphous ice undergoes a pronounced change of structure, ranging from the low-density amorphous ice (LDA) at p=0, through a continuum of HDA states to the limiting very high-density amorphous ice (VHDA) regime above 10 kbar. The main part of the overall structural change takes place within the HDA megabasin, which includes a variety of structures with quite different local and medium-range order as well as network topology and spans a broad range of densities. The VHDA represents the limit to densification by adapting the hydrogen-bonded network topology, without creating interpenetrating networks. The connection between structure and metastability of various forms upon decompression and heating is studied and discussed. We also discuss the analogy with amorphous and crystalline silica. Finally, some conclusions concerning the relation between amorphous ice and supercooled water are drawn.

cond-mat.stat-mech↗

arXiv2004

Simulation of structural phase transitions by metadynamics

We describe here in detail the recently introduced methodology for simulation of structural transitions in crystals. The applications of the new scheme are illustrated on various kinds of crystals and the advantages with respect to previous schemes are emphasized. The relevance of the new method for the problem of crystal structure prediction is also discussed.

cond-mat.mtrl-sci↗

arXiv2004

Polyamorphism of ice at low temperatures from constant-pressure simulations

We report results of MD simulations of amorphous ice in the pressure range 0 - 22.5 kbar. The high-density amorphous ice (HDA) prepared by compression of Ih ice at T = 80 K is annealed to T = 170 K at intermediate pressures in order to generate relaxed states. We confirm the existence of recently observed phenomena, the very high-density amorphous ice and a continuum of HDA forms. We suggest that both phenomena have their origin in the evolution of the network topology of the annealed HDA phase with decreasing volume, resulting at low temperatures in the metastability of a range of densities.

cond-mat.mtrl-sci↗

arXiv2002

Predicting crystal structures: the Parrinello-Rahman method revisited

By suitably adapting a recent approach [A. Laio and M. Parrinello, PNAS, 99, 12562 (2002)] we develop a powerful molecular dynamics method for the study of pressure-induced structural transformations. We use the edges of the simulation cell as collective variables. In the space of these variables we define a metadynamics that drives the system away from the local minimum towards a new crystal structure. In contrast to the Parrinello-Rahman method our approach shows no hysteresis and crystal structure transformations can occur at the equilibrium pressure. We illustrate the power of the method by studying the pressure-induced diamond to simple hexagonal phase transition in a model of silicon.

cond-mat.mtrl-sci↗

arXiv2002

Escaping free-energy minima

We introduce a novel and powerful method for exploring the properties of the multidimensional free energy surfaces of complex many-body systems by means of a coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates.A characteristic feature of this dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the free energy surface, allowing the efficient exploration and accurate determination of the free energy surface 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.

cond-mat.stat-mech↗

arXiv2001

Action-derived molecular dynamics in the study of rare events

We present a practical method to generate classical trajectories with fixed initial and final boundary conditions. Our method is based on the minimization of a suitably defined discretized action. The method finds its most natural application in the study of rare events. Its capabilities are illustrated by non-trivial examples. The algorithm lends itself to straightforward parallelization, and when combined with molecular dynamics (MD) it promises to offer a powerful tool for the study of chemical reactions.

cond-mat.soft↗

arXiv2000

An anomalous alloy: Y_x Si_{1-x}

We study via density functional-based molecular dynamics the structural and dynamical properties of the rare earth silicon amorphous alloy Y_xSi_{1-x} for x=0.093 and x=0.156. The Si network forms cavities in which a Y^{3+} cation is entrapped. Its electrons are transferred to the Si network and are located in the dangling bonds of the Si atoms that line the Y cavities. This leads to the presence of low coordinated Si atoms that can be described as monovalent or divalent anions. For x=0.156, the cavities touch each other and share Si atoms that have two dangling bonds. The vibrational spectrum is similar to that of amorphous Si. However, doping induces a shoulder at 70 cm^{-1} and a pronounced peak at 180 cm^{-1} due to low coordinated Si.

cond-mat.mtrl-sci↗

arXiv1993

Structural Phase Trasformations via Ab-Initio Molecular Dynamics

Available simulation methods, suitable to describe solid-solid phase transitions occurring upon increasing of presssure and/or temperature, are based on empirical interatomic potentials: this restriction reduces the predictive power, and thus the general usefulness of numeric simulations in this very relevant field. We present a new simulation scheme which allows, for the first time, the simulation of these phenomena with the correct quantum-mechanical description of interatomic forces and internal stress, along with the correct statistical mechanics of ionic degrees of freedom. The method is obtained by efficiently combining the Car-Parrinello method for ab- initio molecular dynamics with the Parrinello Rahman method to account for a variable cell shape. Within this scheme phase trasformations may spontaneously take place during the simulation with variation of external pressure and/or temperature. The validity of the method is demonstrated by simulating the metal-insulator transition in Silicon (from diamond structure to simple hexagonal structure) under high pressure.

cond-mat↗