https://www.zora.uzh.ch/id/eprint/3175/3/PP_VandeVondele_CPCom_2005QuickManVO.pdf

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

We present a library of Gaussian basis sets that has been specifically optimized to perform accurate molecular calculations based on density functional theory. It targets a wide range of chemical environments, including the gas phase, interfaces, and the condensed phase. These generally contracted basis sets, which include diffuse primitives, are obtained minimizing a linear combination of the total energy and the condition number of the overlap matrix for a set of molecules with respect to the exponents and contraction coefficients of the full basis. Typically, for a given accuracy in the total energy, significantly fewer basis functions are needed in this scheme than in the usual split valence scheme, leading to a speedup for systems where the computational cost is dominated by diagonalization. More importantly, binding energies of hydrogen bonded complexes are of similar quality as the ones obtained with augmented basis sets, i.e., have a small (down to 0.2 kcal/mol) basis set superposition error, and the monomers have dipoles within 0.1 D of the basis set limit. However, contrary to typical augmented basis sets, there are no near linear dependencies in the basis, so that the overlap matrix is always well conditioned, also, in the condensed phase. The basis can therefore be used in first principles molecular dynamics simulations and is well suited for linear scaling calculations.

/pdf/gaussian-basis-sets-for-accurate-calculations-on-molecular-4u575sk1p4.pdf

Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases.

cp2k has become a versatile open-source tool for the simulation of complex systems on the nanometer scale. It allows for sampling and exploring potential energy surfaces that can be computed using a variety of empirical and first principles models. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern and massively parallel hardware. This review briefly summarizes the main capabilities and illustrates with recent applications the science cp2k has enabled in the field of atomistic simulation.

/pdf/cp2k-atomistic-simulations-of-condensed-matter-systems-12mcj86s5y.pdf

cp2k: atomistic simulations of condensed matter systems

In the last decade, ab initio simulations and especially Car-Parrinello molecular dynamics have significantly contributed to the improvement of our understanding of both the physical and chemical properties of water, ice, and hydrogen-bonded systems in general. At the heart of this family of in silico techniques lies the crucial idea of computing the many-body interactions by solving the electronic structure problem "on the fly" as the simulation proceeds, which circumvents the need for pre-parameterized potential models. In particular, the field of proton transfer in hydrogen-bonded networks greatly benefits from these technical advances. Here, several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.

Proton transfer 200 years after von Grotthuss: insights from ab initio simulations.

The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on expe...

/pdf/force-field-benchmark-of-organic-liquids-density-enthalpy-of-4y1tlrv4sb.pdf

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

A series of first principles molecular dynamics and Monte Carlo simulations were carried out for liquid water to investigate the reproducibility of different sampling approaches. These simulations include Car−Parrinello molecular dynamics simulations using the program cpmd with different values of the fictitious electron mass in the microcanonical and canonical ensembles, Born−Oppenheimer molecular dynamics using the programs cpmd and cp2k in the microcanonical ensemble, and Metropolis Monte Carlo using cp2k in the canonical ensemble. With the exception of one simulation for 128 water molecules, all other simulations were carried out for systems consisting of 64 molecules. Although the simulations yield somewhat fortuitous agreement in structural properties, analysis of other properties demonstrate that one should exercise caution when assuming the reproducibility of Car−Parrinello and Born−Oppenheimer molecular dynamics simulations for small system sizes in the microcanonical ensemble. In contrast, the m...

Liquid Water from First Principles: Investigation of Different Sampling Approaches

The acetonitrile/anatase(101) interface can be considered a prototypical interface between an oxide and a polar aprotic liquid, and is common in dye sensitized solar cells. Using first principles molecular dynamics simulations of a slab of TiO2 in contact with neat acetonitrile (MeCN), the liquid structure near this interface has been characterized. Furthermore, in order to investigate properties that require extensive sampling, a classical force field to describe the MeCN/TiO2 interaction has been optimized, and we show that this force field accurately describes the structure near the interface. We find a surprisingly strong interaction of MeCN with TiO2, which leads to an ordered first MeCN layer displaying a significantly enhanced molecular dipole. The strong dipolar interactions between solvent molecules lead to pronounced layering further away from the interface, each successive layer having an alternate orientation of the molecular dipoles. At least seven distinct solvent layers (approximately 12 angstrom) can be discerned in the orientational distribution function. The observed structure also strongly suppresses diffusion parallel to the interface in the first nanometer of the liquid. These results show that the properties of the liquid near the interface differ from those in the bulk, which suggests that solvation near the interface will be distinctly different from solvation in the bulk.

/pdf/atomistic-simulations-of-a-solid-liquid-interface-a-combined-4em4h886g2.pdf

Atomistic simulations of a solid/liquid interface: a combined force field and first principles approach to the structure and dynamics of acetonitrile near an anatase surface

Jiirg Hutter

Papers

Liquid Water from First Principles: Investigation of Different Sampling Approaches

Atomistic simulations of a solid/liquid interface: a combined force field and first principles approach to the structure and dynamics of acetonitrile near an anatase surface