/pdf/scalable-molecular-dynamics-with-namd-3j7xyc70g4.pdf

Scalable Molecular Dynamics with NAMD

First-principles simulation, meaning density-functional theory calculations with plane waves and pseudopotentials, has become a prized technique in condensed-matter theory. Here I look at the basics of the suject, give a brief review of the theory, examining the strengths and weaknesses of its implementation, and illustrating some of the ways simulators approach problems through a small case study. I also discuss why and how modern software design methods have been used in writing a completely new modular version of the CASTEP code.

https://iopscience.iop.org/article/10.1088/0953-8984/14/11/301/pdf

First-principles simulation: ideas, illustrations and the CASTEP code

https://zenodo.org/record/1258869/files/article.pdf

NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations

Ionization of highly compressed ammonia has previously been predicted by computation. Here, the authors provide experimental evidence for this autoionization process at high pressures, showing the transformation of molecular ammonia into ammonium amide.

/pdf/ammonia-as-a-case-study-for-the-spontaneous-ionization-of-a-43dukoq5c2.pdf

Ammonia as a case study for the spontaneous ionization of a simple hydrogen-bonded compound

On the development of proton conducting polymer membranes for hydrogen and methanol fuel cells

Explanations for the anomalously high mobility of protons in liquid water began with Grotthuss's idea1, 2 of ‘structural diffusion’ nearly two centuries ago Subsequent explanations have refined this concept by invoking thermal hopping3, 4, proton tunnelling5, 6 or solvation effects7 More recently, two main structural models have emerged for the hydrated proton Eigen8, 9 proposed the formation of an H9O4+ complex in which an H3O+ core is strongly hydrogen-bonded to three H2O molecules Zundel10, 11, meanwhile, supported the notion of an H5O2+ complex in which the proton isshared between two H2O molecules Here we use ab initio path integral12,13,14 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’15, 16, 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

The nature of the hydrated excess proton in water

Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques in order that readers can understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely-used Car-Parrinello approach, correcting various misconceptions currently found in research literature. The book also contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly-used program packages, and enabling developers to improve and add new features in their code. 

• Discusses the Car-Parrinello approach and its special features helping to correct various misconceptions currently found in research literature • Allows readers to understand widely used program packages and to improve their own programs by featuring pseudo-code and program layout • Enables readers to assess the pros and cons of commonly used ab initio simulation methods by including systematic derivations of ab initio molecular dynamics schemes

Ab initio molecular dynamics: basic theory and advanced methods

The relative influence of thermal and quantum fluctuations on the proton transfer properties of the charged water complexes H5O2+ and H3O2− was investigated with the use of ab initio techniques. These small systems can be considered as prototypical representatives of strong and intermediate-strength hydrogen bonds. The shared proton in the strongly hydrogen bonded H5O2+ behaved in an essentially classical manner, whereas in the H3O2− low-barrier hydrogen bond, quantum zero-point motion played a crucial role even at room temperature. This behavior can be traced back to a small difference in the oxygen-oxygen separation and hence to the strength of the hydrogen bond.

https://science.sciencemag.org/content/sci/275/5301/817.full.pdf

On the quantum nature of the shared proton in hydrogen bonds

Preface 1. Setting the stage: why ab initio molecular dynamics? Part I. Basic Techniques: 2. Getting started: unifying MD and electronic structure 3. Implementation: using the plane wave basis set 4. Atoms with plane waves: accurate pseudopotentials Part II. Advanced Techniques: 5. Beyond standard ab initio molecular dynamics 6. Beyond norm-conserving pseudopotentials 7. Computing properties 8. Parallel computing Part III. Applications: 9. From materials to biomolecules 10. Properties from ab initio simulations 11. Outlook Bibliography Index.

https://assets.cambridge.org/97811076/63534/frontmatter/9781107663534_frontmatter.pdf

Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods

The essential ideas underlying ab initio path integral molecular dynamics and its efficient numerical implementation are discussed. In this approach the nuclei are treated as quantum particles within the path integral formulation of quantum statistical mechanics. The electronic degrees of freedom are treated explicitly based on state‐of‐the‐art electronic structure theory. This renders ab initio simulations of quantum systems possible without recourse to model potentials. A combined extended Lagrangian for both quantum nuclei and electrons defines a dynamical system and yields molecular dynamics trajectories that can be analyzed to obtain quantum statistical expectation values of time‐independent operators. The methodology can be applied to a wide range of fields addressing problems in molecular and condensed matter chemistry and physics.

Dominik Marx

Papers

The nature of the hydrated excess proton in water

Ab initio molecular dynamics: basic theory and advanced methods

On the quantum nature of the shared proton in hydrogen bonds

Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods

Ab initio path integral molecular dynamics : basic ideas