GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package originally developed in the University of Groningen, now maintained and extended at different places, including the University of Uppsala, University of Stockholm and the Max Planck Institute for Polymer Research. Molecular dynamics ( MD) is a form of Computer simulation in which atoms and molecules are allowed to interact for a period of time by approximations of The University of Groningen (Rijksuniversiteit Groningen located in the city of Groningen, was founded in 1614. Uppsala University ( Swedish Uppsala universitet) is a world-class research University in Uppsala, Sweden. Stockholm University ( Stockholms universitet) is a state University in Stockholm, Sweden. The Max Planck Institute for Polymer Research ( German: Max-Planck-Institut für Polymerforschung) is a scientific research intitute located in Mainz, [1][2]
The GROMACS project was originally started to construct a dedicated parallel computer system for molecular simulations, based on a ring architecture. The molecular dynamics specific routines were rewritten in the C programming language from the Fortran77-based program GROMOS, which had been developed in the same group. tags please moot on the talk page first! --> In Computing, C is a general-purpose cross-platform block structured Fortran (previously FORTRAN) is a general-purpose, procedural, imperative Programming language that is especially suited to GROMOS is a force field for Molecular dynamics Simulation developed at the University of Groningen and the ETH Zurich. However, many specific elements were added, most notably:
- computation of the virial in a single, rather than in a double sum over particles,
- generic representation of all possible periodic box types as triclinic,
- optimized handling of the neighbor list by storage of translation vectors to the nearest neighbor in a periodic system,
- a specialized routine for the calculation of the inverse square root,
- the use of cubic spline interpolation from tabulated values for the evaluation of force/energy,
- a fast grid-based neighbor searching,
- the use of multimedia (3DNow! and SSE) instructions on Pentium (III and higher), Athlon, and Duron processors. In Mechanics, the virial theorem provides a general equation relating the average total Kinetic energy, \left\langle T \right\rangle of a stable system In Crystallography, the triclinic Crystal system is one of the 7 lattice Point groups A crystal system is described by three basis vectors Multimedia is media and content that utilizes a combination of different content forms. 3DNow! is the Trade name of a multimedia extension created by AMD for its processors starting with the K6-2 in 1998 The Pentium brand refers to Intel 's single-core x86 Microprocessor based on the P5 fifth-generation Microarchitecture. Athlon is the brand name applied to a series of different X86 processors designed and manufactured by AMD. The AMD Duron was an X86 -compatible Computer processor manufactured by AMD.
The highly optimized code makes GROMACS the fastest program for molecular simulations to date. In addition, support for different force fields and the open source (GPL) nature of the project make GROMACS very flexible. In the context of Molecular mechanics, a force field (also called a forcefield) refers to the functional form and Parameter sets used Open source is a development methodology which offers practical accessibility to a product's source (goods and knowledge A notable use of GROMACS is in the distributed computing project Folding@Home, where it is used extensively in the simulation of protein folding. Distributed computing deals with Hardware and Software Systems containing more than one processing element or Storage element concurrent Folding@home (sometimes abbreviated as FAH or F@h) is a Distributed computing (DC project designed to perform computationally intensive simulations Protein folding is the physical process by which a Polypeptide folds into its characteristic and functional three-dimensional structure. (This version has been granted a non-GPL license. [1])
References
- ^ Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005). "GROMACS: fast, flexible, and free". J Comput Chem 26 (16): 1701–18. doi:. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document. PMID 16211538.
- ^ Hess B, Kutzner C, Van Der Spoel D, Lindahl E (2008). "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation". J Chem Theory Comput 4 (2): 435. doi:. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document.
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The OPLS (Optimized Potential for Liquid Simulations force field was developed by Prof GROMOS is a force field for Molecular dynamics Simulation developed at the University of Groningen and the ETH Zurich. CHARMM ( Chemistry at HARvard Macromolecular Mechanics) is the name of a widely used set of force fields for Molecular dynamics as well as the NAMD ( NA noscale M olecular D ynamics1is a free-of-charge Molecular dynamics simulation package written using the Charm++ Grace stands for "GRaphing Advanced Computation and Exploration of data Folding@home (sometimes abbreviated as FAH or F@h) is a Distributed computing (DC project designed to perform computationally intensive simulationsDapyx Software network: MP3 Explorer | Ebook Manager | Zenithic