Force field (chemistry)In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both.
Molecular dynamicsMolecular 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.
SupercomputerA supercomputer is a computer with a high level of performance as compared to a general-purpose computer. The performance of a supercomputer is commonly measured in floating-point operations per second (FLOPS) instead of million instructions per second (MIPS). Since 2017, there have existed supercomputers which can perform over 1017 FLOPS (a hundred quadrillion FLOPS, 100 petaFLOPS or 100 PFLOPS). For comparison, a desktop computer has performance in the range of hundreds of gigaFLOPS (1011) to tens of teraFLOPS (1013).
Molecular modellingMolecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.
High-performance computingHigh-performance computing (HPC) uses supercomputers and computer clusters to solve advanced computation problems. HPC integrates systems administration (including network and security knowledge) and parallel programming into a multidisciplinary field that combines digital electronics, computer architecture, system software, programming languages, algorithms and computational techniques. HPC technologies are the tools and systems used to implement and create high performance computing systems.
Computer performanceIn computing, computer performance is the amount of useful work accomplished by a computer system. Outside of specific contexts, computer performance is estimated in terms of accuracy, efficiency and speed of executing computer program instructions. When it comes to high computer performance, one or more of the following factors might be involved: Short response time for a given piece of work. High throughput (rate of processing work). Low utilization of computing resource(s). Fast (or highly compact) data compression and decompression.
Density functional theoryDensity-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (or nuclear structure) (principally the ground state) of many-body systems, in particular atoms, molecules, and the condensed phases. Using this theory, the properties of a many-electron system can be determined by using functionals, i.e. functions of another function. In the case of DFT, these are functionals of the spatially dependent electron density.
Molecular mechanicsMolecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms.
Computational chemistryComputational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form.
GROMACSGROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide. GROMACS is one of the fastest and most popular software packages available, and can run on central processing units (CPUs) and graphics processing units (GPUs). It is free, open-source software released under the GNU General Public License (GPL), and starting with version 4.
Computer clusterA computer cluster is a set of computers that work together so that they can be viewed as a single system. Unlike grid computers, computer clusters have each node set to perform the same task, controlled and scheduled by software. The components of a cluster are usually connected to each other through fast local area networks, with each node (computer used as a server) running its own instance of an operating system. In most circumstances, all of the nodes use the same hardware and the same operating system, although in some setups (e.
BiophysicsBiophysics is an interdisciplinary science that applies approaches and methods traditionally used in physics to study biological phenomena. Biophysics covers all scales of biological organization, from molecular to organismic and populations. Biophysical research shares significant overlap with biochemistry, molecular biology, physical chemistry, physiology, nanotechnology, bioengineering, computational biology, biomechanics, developmental biology and systems biology. The term biophysics was originally introduced by Karl Pearson in 1892.
Distributed computingA distributed system is a system whose components are located on different networked computers, which communicate and coordinate their actions by passing messages to one another. Distributed computing is a field of computer science that studies distributed systems. The components of a distributed system interact with one another in order to achieve a common goal. Three significant challenges of distributed systems are: maintaining concurrency of components, overcoming the lack of a global clock, and managing the independent failure of components.
Electron densityElectron density or electronic density is the measure of the probability of an electron being present at an infinitesimal element of space surrounding any given point. It is a scalar quantity depending upon three spatial variables and is typically denoted as either or . The density is determined, through definition, by the normalised -electron wavefunction which itself depends upon variables ( spatial and spin coordinates). Conversely, the density determines the wave function modulo up to a phase factor, providing the formal foundation of density functional theory.
Reconfigurable computingReconfigurable computing is a computer architecture combining some of the flexibility of software with the high performance of hardware by processing with very flexible high speed computing fabrics like field-programmable gate arrays (FPGAs). The principal difference when compared to using ordinary microprocessors is the ability to make substantial changes to the datapath itself in addition to the control flow. On the other hand, the main difference from custom hardware, i.e.
Hyper-threadingHyper-threading (officially called Hyper-Threading Technology or HT Technology and abbreviated as HTT or HT) is Intel's proprietary simultaneous multithreading (SMT) implementation used to improve parallelization of computations (doing multiple tasks at once) performed on x86 microprocessors. It was introduced on Xeon server processors in February 2002 and on Pentium 4 desktop processors in November 2002. Since then, Intel has included this technology in Itanium, Atom, and Core 'i' Series CPUs, among others.
Test suiteIn software development, a test suite, less commonly known as a validation suite, is a collection of test cases that are intended to be used to test a software program to show that it has some specified set of behaviors. A test suite often contains detailed instructions or goals for each collection of test cases and information on the system configuration to be used during testing. A group of test cases may also contain prerequisite states or steps, and descriptions of the following tests.
Thread (computing)In computer science, a thread of execution is the smallest sequence of programmed instructions that can be managed independently by a scheduler, which is typically a part of the operating system. The implementation of threads and processes differs between operating systems. In Modern Operating Systems, Tanenbaum shows that many distinct models of process organization are possible. In many cases, a thread is a component of a process.
Information managementInformation management (IM) is the appropriate and optimized capture, storage, retrieval, and use of information. It may be personal information management or organizational. IM for organizations concerns a cycle of organizational activity: the acquisition of information from one or more sources, the custodianship and the distribution of that information to those who need it, and its ultimate disposal through archiving or deletion.
