en.unionpedia.org

OpenMM, the Glossary

OpenMM is a library for performing molecular dynamics simulations on a wide variety of hardware architectures.^[1]

37 relations: AMBER, Bennett acceptance ratio, Brownian motion, C (programming language), C++, CHARMM, Comparison of force-field implementations, Comparison of software for molecular mechanics modeling, COVID-19 pandemic, CUDA, Folding@home, Force field (chemistry), GNU Lesser General Public License, Grace (plotting tool), Graphics processing unit, GROMACS, LAMMPS, Langevin equation, Linux, MacOS, Memorial Sloan Kettering Cancer Center, Microsoft Windows, MIT License, Molecular design software, Molecular dynamics, NAMD, National Heart, Lung, and Blood Institute, Nosé–Hoover thermostat, Numerical integration, OpenCL, Pompeu Fabra University, Protein dynamics, Python (programming language), Stanford University, Verlet integration, Vijay S. Pande, Wrapper library.
Molecular dynamics software

AMBER

Assisted Model Building with Energy Refinement (AMBER) is the name of a widely-used molecular dynamics software package originally developed by Peter Kollman's group at the University of California, San Francisco. OpenMM and AMBER are molecular dynamics software.

See OpenMM and AMBER

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 OpenMM and Bennett acceptance ratio

Brownian motion

Brownian motion is the random motion of particles suspended in a medium (a liquid or a gas).

See OpenMM and Brownian motion

C (programming language)

C (pronounced – like the letter c) is a general-purpose programming language.

See OpenMM 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 OpenMM and C++

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. OpenMM and CHARMM are molecular dynamics software.

See OpenMM and CHARMM

Comparison of force-field implementations

This is a table of notable computer programs implementing molecular mechanics force fields.

See OpenMM 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. OpenMM and Comparison of software for molecular mechanics modeling are molecular dynamics software.

See OpenMM and Comparison of software for molecular mechanics modeling

COVID-19 pandemic

The COVID-19 pandemic (also known as the coronavirus pandemic), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), began with an outbreak of COVID-19 in Wuhan, China, in December 2019.

See OpenMM and COVID-19 pandemic

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 OpenMM and CUDA

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. OpenMM and Folding@home are molecular dynamics software.

See OpenMM and Folding@home

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 OpenMM and Force field (chemistry)

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 OpenMM and GNU Lesser General Public License

Grace is a free WYSIWYG 2D graph plotting tool, for Unix-like operating systems.

See OpenMM 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 OpenMM and Graphics processing unit

GROMACS

GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. OpenMM and GROMACS are free software programmed in C and molecular dynamics software.

See OpenMM and GROMACS

LAMMPS

Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. OpenMM and LAMMPS are molecular dynamics software.

See OpenMM and LAMMPS

Langevin equation

In physics, a Langevin equation (named after Paul Langevin) is a stochastic differential equation describing how a system evolves when subjected to a combination of deterministic and fluctuating ("random") forces.

See OpenMM and Langevin equation

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. OpenMM and Linux are free software programmed in C.

See OpenMM and Linux

MacOS

macOS, originally Mac OS X, previously shortened as OS X, is an operating system developed and marketed by Apple since 2001.

See OpenMM and MacOS

Memorial Sloan Kettering Cancer Center

Memorial Sloan Kettering Cancer Center (MSK or MSKCC) is a cancer treatment and research institution in Manhattan in New York City.

See OpenMM and Memorial Sloan Kettering Cancer Center

Microsoft Windows

Microsoft Windows is a product line of proprietary graphical operating systems developed and marketed by Microsoft.

See OpenMM and Microsoft Windows

MIT License

The MIT License is a permissive software license originating at the Massachusetts Institute of Technology (MIT) in the late 1980s.

See OpenMM and MIT License

Molecular design software

Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. OpenMM and molecular design software are molecular dynamics software.

See OpenMM and Molecular design software

Molecular dynamics

Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules.

See OpenMM 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). OpenMM and NAMD are molecular dynamics software.

See OpenMM and NAMD

National Heart, Lung, and Blood Institute

The National Heart, Lung, and Blood Institute (NHLBI) is the third largest Institute of the National Institutes of Health, located in Bethesda, Maryland, United States.

See OpenMM and National Heart, Lung, and Blood Institute

Nosé–Hoover thermostat

The Nosé–Hoover thermostat is a deterministic algorithm for constant-temperature molecular dynamics simulations.

See OpenMM and Nosé–Hoover thermostat

Numerical integration

In analysis, numerical integration comprises a broad family of algorithms for calculating the numerical value of a definite integral.

See OpenMM and Numerical integration

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.

See OpenMM and OpenCL

References

[1] https://en.wikipedia.org/wiki/OpenMM

OpenMM, the Glossary

Table of Contents

See also

Molecular dynamics software

References