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.
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.
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.
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.
Molecular design softwareMolecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g
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).
Multi-core processorA multi-core processor is a microprocessor on a single integrated circuit with two or more separate processing units, called cores, each of which reads and executes program instructions. The instructions are ordinary CPU instructions (such as add, move data, and branch) but the single processor can run instructions on separate cores at the same time, increasing overall speed for programs that support multithreading or other parallel computing techniques.
Parallel computingParallel computing is a type of computation in which many calculations or processes are carried out simultaneously. Large problems can often be divided into smaller ones, which can then be solved at the same time. There are several different forms of parallel computing: bit-level, instruction-level, data, and task parallelism. Parallelism has long been employed in high-performance computing, but has gained broader interest due to the physical constraints preventing frequency scaling.
Communication protocolA communication protocol is a system of rules that allows two or more entities of a communications system to transmit information via any variation of a physical quantity. The protocol defines the rules, syntax, semantics, and synchronization of communication and possible error recovery methods. Protocols may be implemented by hardware, software, or a combination of both. Communicating systems use well-defined formats for exchanging various messages.
Application layerAn application layer is an abstraction layer that specifies the shared communications protocols and interface methods used by hosts in a communications network. An application layer abstraction is specified in both the Internet Protocol Suite (TCP/IP) and the OSI model. Although both models use the same term for their respective highest-level layer, the detailed definitions and purposes are different. In the Internet protocol suite, the application layer contains the communications protocols and interface methods used in process-to-process communications across an Internet Protocol (IP) computer network.
