GROMACS, the Glossary
GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids.[1]
Table of Contents
55 relations: Abalone (molecular mechanics), Artificial life, Backronym, Bennett acceptance ratio, Biochemistry, C (programming language), C++, Central processing unit, CHARMM, Command-line interface, Comparison of force-field implementations, Comparison of software for molecular mechanics modeling, CUDA, Distributed computing, Estimated time of arrival, Folding@home, Force field (chemistry), Fortran, GNU General Public License, GNU Lesser General Public License, Grace (plotting tool), Graphics processing unit, GROMOS, KTH Royal Institute of Technology, LAMMPS, Linux, Lipid, List of Folding@home cores, MacOS, Message Passing Interface, Microsoft Windows, Molecular design software, Molecular dynamics, NAMD, Netherlands, Nucleic acid, Open-source software, OpenCL, OpenMM, OPLS, Protein, Protein Data Bank, Protein folding, Rosetta@home, Solvent, Stanford University, Sweden, SYCL, Thread (computing), University of Groningen, ... Expand index (5 more) »
- Molecular dynamics software
Abalone (molecular mechanics)
Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit (flexible SPC water model) or in implicit water models. GROMACS and Abalone (molecular mechanics) are molecular dynamics software.
See GROMACS and Abalone (molecular mechanics)
Artificial life
Artificial life (ALife or A-Life) is a field of study wherein researchers examine systems related to natural life, its processes, and its evolution, through the use of simulations with computer models, robotics, and biochemistry.
See GROMACS and Artificial life
Backronym
A backronym is an acronym formed from an already existing word by expanding its letters into the words of a phrase.
Bennett acceptance ratio
The Bennett acceptance ratio method (BAR) is an algorithm for estimating the difference in free energy between two systems (usually the systems will be simulated on the computer).
See GROMACS and Bennett acceptance ratio
Biochemistry
Biochemistry or biological chemistry is the study of chemical processes within and relating to living organisms.
C (programming language)
C (pronounced – like the letter c) is a general-purpose programming language.
See GROMACS and C (programming language)
C++
C++ (pronounced "C plus plus" and sometimes abbreviated as CPP) is a high-level, general-purpose programming language created by Danish computer scientist Bjarne Stroustrup.
See GROMACS and C++
Central processing unit
A central processing unit (CPU), also called a central processor, main processor, or just processor, is the most important processor in a given computer.
See GROMACS and Central processing unit
CHARMM
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. GROMACS and CHARMM are molecular dynamics software.
Command-line interface
A command-line interface (CLI) is a means of interacting with a computer program by inputting lines of text called command-lines.
See GROMACS and Command-line interface
Comparison of force-field implementations
This is a table of notable computer programs implementing molecular mechanics force fields.
See GROMACS and Comparison of force-field implementations
Comparison of software for molecular mechanics modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations. GROMACS and Comparison of software for molecular mechanics modeling are molecular dynamics software.
See GROMACS and Comparison of software for molecular mechanics modeling
CUDA
In computing, CUDA (originally Compute Unified Device Architecture) is a proprietary parallel computing platform and application programming interface (API) that allows software to use certain types of graphics processing units (GPUs) for accelerated general-purpose processing, an approach called general-purpose computing on GPUs (GPGPU).
See GROMACS and CUDA
Distributed computing
Distributed computing is a field of computer science that studies distributed systems, defined as computer systems whose inter-communicating components are located on different networked computers.
See GROMACS and Distributed computing
Estimated time of arrival
The estimated time of arrival (ETA) is the time when a ship, vehicle, aircraft, cargo, person, or emergency service is expected to arrive at a certain place.
See GROMACS and Estimated time of arrival
Folding@home
Folding@home (FAH or F@h) is a distributed computing project aimed to help scientists develop new therapeutics for a variety of diseases by the means of simulating protein dynamics. GROMACS and Folding@home are molecular dynamics software.
Force field (chemistry)
In the context of chemistry, molecular physics, physical chemistry, and molecular modelling, a force field is a computational model that is used to describe the forces between atoms (or collections of atoms) within molecules or between molecules as well as in crystals.
See GROMACS and Force field (chemistry)
Fortran
Fortran (formerly FORTRAN) is a third generation, compiled, imperative programming language that is especially suited to numeric computation and scientific computing.
GNU General Public License
The GNU General Public License (GNU GPL or simply GPL) is a series of widely used free software licenses, or copyleft, that guarantee end users the four freedoms to run, study, share, and modify the software.
See GROMACS and GNU General Public License
GNU Lesser General Public License
The GNU Lesser General Public License (LGPL) is a free-software license published by the Free Software Foundation (FSF).
See GROMACS and GNU Lesser General Public License
Grace is a free WYSIWYG 2D graph plotting tool, for Unix-like operating systems.
See GROMACS and Grace (plotting tool)
Graphics processing unit
A graphics processing unit (GPU) is a specialized electronic circuit initially designed for digital image processing and to accelerate computer graphics, being present either as a discrete video card or embedded on motherboards, mobile phones, personal computers, workstations, and game consoles.
See GROMACS and Graphics processing unit
GROMOS
GROningen MOlecular Simulation (GROMOS) is the name of a force field for molecular dynamics simulation, and a related computer software package. GROMACS and GROMOS are molecular dynamics software.
KTH Royal Institute of Technology
The KTH Royal Institute of Technology (lit), abbreviated KTH, is a public research university in Stockholm, Sweden.
See GROMACS and KTH Royal Institute of Technology
LAMMPS
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. GROMACS and LAMMPS are molecular dynamics software.
Linux
Linux is both an open-source Unix-like kernel and a generic name for a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. GROMACS and Linux are free software programmed in C.
Lipid
Lipids are a broad group of organic compounds which include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others.
List of Folding@home cores
The distributed-computing project Folding@home uses scientific computer programs, referred to as "cores" or "fahcores", to perform calculations. GROMACS and List of Folding@home cores are molecular dynamics software.
See GROMACS and List of Folding@home cores
MacOS
macOS, originally Mac OS X, previously shortened as OS X, is an operating system developed and marketed by Apple since 2001.
Message Passing Interface
The Message Passing Interface (MPI) is a standardized and portable message-passing standard designed to function on parallel computing architectures.
See GROMACS and Message Passing Interface
Microsoft Windows
Microsoft Windows is a product line of proprietary graphical operating systems developed and marketed by Microsoft.
See GROMACS and Microsoft Windows
Molecular design software
Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. GROMACS and molecular design software are molecular dynamics software.
See GROMACS and Molecular design software
Molecular dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules.
See GROMACS and Molecular dynamics
NAMD
Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program) is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model (not to be confused with CHARMM). GROMACS and NAMD are molecular dynamics software.
See GROMACS and NAMD
Netherlands
The Netherlands, informally Holland, is a country located in Northwestern Europe with overseas territories in the Caribbean.
Nucleic acid
Nucleic acids are large biomolecules that are crucial in all cells and viruses.
Open-source software
Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose.
See GROMACS and Open-source software
OpenCL
OpenCL (Open Computing Language) is a framework for writing programs that execute across heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), digital signal processors (DSPs), field-programmable gate arrays (FPGAs) and other processors or hardware accelerators.
OpenMM
OpenMM is a library for performing molecular dynamics simulations on a wide variety of hardware architectures. GROMACS and OpenMM are free software programmed in C and molecular dynamics software.
OPLS
The OPLS (Optimized Potentials for Liquid Simulations) force field was developed by Prof.
See GROMACS and OPLS
Protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues.
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB).
See GROMACS and Protein Data Bank
Protein folding
Protein folding is the physical process by which a protein, after synthesis by a ribosome as a linear chain of amino acids, changes from an unstable random coil into a more ordered three-dimensional structure.
See GROMACS and Protein folding
Rosetta@home
Rosetta@home is a volunteer computing project researching protein structure prediction on the Berkeley Open Infrastructure for Network Computing (BOINC) platform, run by the Baker lab.
Solvent
A solvent (from the Latin solvō, "loosen, untie, solve") is a substance that dissolves a solute, resulting in a solution.
Stanford University
Stanford University (officially Leland Stanford Junior University) is a private research university in Stanford, California.
See GROMACS and Stanford University
Sweden
Sweden, formally the Kingdom of Sweden, is a Nordic country located on the Scandinavian Peninsula in Northern Europe.
SYCL
SYCL (pronounced "sickle") is a higher-level programming model to improve programming productivity on various hardware accelerators.
See GROMACS and SYCL
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.
See GROMACS and Thread (computing)
University of Groningen
The University of Groningen (abbreviated as UG; Rijksuniversiteit Groningen, abbreviated as RUG) is a public research university of more than 30,000 students in the city of Groningen in the Netherlands.
See GROMACS and University of Groningen
Unix
Unix (trademarked as UNIX) is a family of multitasking, multi-user computer operating systems that derive from the original AT&T Unix, whose development started in 1969 at the Bell Labs research center by Ken Thompson, Dennis Ritchie, and others.
See GROMACS and Unix
Uppsala University
Uppsala University (UU) (Uppsala universitet) is a public research university in Uppsala, Sweden.
See GROMACS and Uppsala University
VisIt
VisIt is an open-source, interactive parallel visualization, and graphical analysis tool designed for viewing scientific data.
VOTCA
Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) is a Coarse-grained modeling package, which focuses on the analysis of molecular dynamics data, the development of systematic coarse-graining techniques as well as methods used for simulating microscopic charge (and exciton) transport in disordered semiconductors. GROMACS and VOTCA are molecular dynamics software.
YASARA
Yet Another Scientific Artificial Reality Application (YASARA) is a computer program for molecular visualising, modelling, and dynamics. GROMACS and YASARA are molecular dynamics software.
See also
Molecular dynamics software
- AMBER
- Abalone (molecular mechanics)
- Amsterdam Density Functional
- Ascalaph Designer
- Avizo (software)
- CHARMM
- CP2K
- Car–Parrinello molecular dynamics
- Comparison of nucleic acid simulation software
- Comparison of software for molecular mechanics modeling
- D. E. Shaw Research
- Desmond (software)
- Folding@home
- GROMACS
- GROMOS
- LAMMPS
- List of Folding@home cores
- MBN Explorer
- MDynaMix
- MacroModel
- Molecular Modelling Toolkit
- Molecular design software
- Ms2 (software)
- NAMD
- OpenAtom
- OpenMM
- Orac (MD program)
- PLUMED
- Pydlpoly
- Q (software)
- SHARC molecular dynamics software
- Tinker (software)
- VOTCA
- Winmostar
- X-PLOR
- XMD
- YASARA
References
[1] https://en.wikipedia.org/wiki/GROMACS
Also known as Gromacs MD, Gromacs MD code.
, Unix, Uppsala University, VisIt, VOTCA, YASARA.