Publication

Simulations of enzymatic systems: Perspectives from Car-Parrinello molecular dynamics simulations

2001
Book Chapters

Abstract

A review with 184 refs. The authors review the principles of the Car-Parrinello method for ab initio mol. dynamics (AIMD) simulations by first outlining the foundations of the method based on d. functional theory, plane wave basis sets and pseudopotentials. Next they outline the approaches of AIMD to modeling of biol. systems with an emphasis on enzymes. Finally they provide an outlook for future directions for the investigation of enzymes and other classes of biomols. [on SciFinder (R)]

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2001
Book Chapters

Abstract

Official source

Related concepts (29)

Molecular dynamics

Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.

System

A system is a group of interacting or interrelated elements that act according to a set of rules to form a unified whole. A system, surrounded and influenced by its environment, is described by its boundaries, structure and purpose and is expressed in its functioning. Systems are the subjects of study of systems theory and other systems sciences. Systems have several common properties and characteristics, including structure, function(s), behavior and interconnectivity.

Simulation

A simulation is the imitation of the operation of a real-world process or system over time. Simulations require the use of models; the model represents the key characteristics or behaviors of the selected system or process, whereas the simulation represents the evolution of the model over time. Often, computers are used to execute the simulation. Simulation is used in many contexts, such as simulation of technology for performance tuning or optimizing, safety engineering, testing, training, education, and video games.

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Simulations of enzymatic systems: Perspectives from Car-Parrinello molecular dynamics simulations

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