Search Results for "molecular dynamics software"
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Showing 418 open source projects for "molecular dynamics software"
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QMCF2
Quantum Mechanical Charge Field - Molecular Dynamics
The Quantum Mechanical Charge Field - Molecular Dynamics package in it's second (improved) version. Developed at the University of Innsbruck, Austria. -
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Chemical Trajectory Analyzer
A software package for processing and analyzing chemical trajectories
ChemTraYzer creates reaction models from molecular dynamics simulations. It's available as open software (MIT license). Please find a full description @ https://www.ltt.rwth-aachen.de/cms/LTT/Forschung/Forschung-am-LTT/Model-Based-Fuel-Design/Aktuelle-Projekte/~kqbf/ChemTraYzer/lidx/1 M.Döntgen, M.-D.Przybylski-Freund, L.C.Kröger, W.A.Kopp, A.E.Ismail, K.Leonhard, "Automated Discovery of Reaction Pathways, Rate Constants, and Transition States Using Reactive Molecular Dynamics Simulations", J. ... -
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Molly.jl
Molecular simulation in Julia
Much of science can be explained by the movement and interaction of molecules. Molecular dynamics (MD) is a computational technique used to explore these phenomena, from noble gases to biological macromolecules. Molly.jl is a pure Julia package for MD, and for the simulation of physical systems more broadly. The package is described in a talk at Enzyme Conference 2023 and an earlier talk at the JuliaMolSim minisymposium at JuliaCon 2022. -
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FairChem
FAIR Chemistry's library of machine learning methods for chemistry
...Version 2 modernizes the stack with a cleaner core package and breaking changes relative to V1, focusing on simpler installs and a stable API surface for production and research. The centerpiece models (e.g., UMA variants) plug directly into the ASE ecosystem via a FAIRChem calculator, so users can run relaxations, molecular dynamics, spin-state energetics, and surface catalysis workflows with the same pretrained network by switching a task flag. Tasks span heterogeneous domains—catalysis (OC20-style), inorganic materials (OMat), molecules (OMol), MOFs (ODAC), and molecular crystals (OMC)—allowing one model family to serve many simulations. The README provides quick paths for pulling models (e.g., via Hugging Face access), then running energy/force predictions on GPU or CPU. -
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Oceananigans.jl
Julia software for fast, friendly, flexible fluid dynamics on CPUs
Oceananigans is a fast, friendly, flexible software package for finite volume simulations of the nonhydrostatic and hydrostatic Boussinesq equations on CPUs and GPUs. It runs on GPUs (wow, fast!), though we believe Oceananigans makes the biggest waves with its ultra-flexible user interface that makes simple simulations easy, and complex, creative simulations possible. -
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QuTiP
QuTiP: Quantum Toolbox in Python
QuTiP is open-source software for simulating the dynamics of open quantum systems. The QuTiP library depends on the excellent Numpy, Scipy, and Cython numerical packages. In addition, graphical output is provided by Matplotlib. QuTiP aims to provide user-friendly and efficient numerical simulations of a wide variety of Hamiltonians, including those with arbitrary time-dependence, commonly found in a wide range of physics applications such as quantum optics, trapped ions, superconducting circuits, and quantum nanomechanical resonators. ... -
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DynamicalSystems.jl
Award winning software library for nonlinear dynamics timeseries
DynamicalSystems.jl is an award-winning Julia software library for nonlinear dynamics and nonlinear time series analysis. To install DynamicalSystems.jl, run import Pkg; Pkg.add("DynamicalSystems"). To learn how to use it and see its contents visit the documentation, which you can either find online or build locally by running the docs/make.jl file. DynamicalSystems.jl is part of JuliaDynamics, an organization dedicated to creating high-quality scientific software. ... -
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BioEmu
Inference code for scalable emulation of protein equilibrium ensembles
...To reconstruct the side-chains, several tools are available. As an example, we interface with HPacker to conduct side-chain reconstruction and also provide basic tooling for running a short molecular dynamics (MD) equilibration. -
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JSBSim
An open source flight dynamics & control software library
JSBSim is a multi-platform, general purpose object-oriented Flight Dynamics Model (FDM) written in C++. The FDM is essentially the physics & math model that defines the movement of an aircraft, rocket, etc., under the forces and moments applied to it using the various control mechanisms and from the forces of nature. JSBSim can be run in a standalone batch mode flight simulator (no graphical displays a.k.a. console mode) for testing and study, or integrated with the Unreal engine, FlightGear... -
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Symbolics.jl
Symbolic programming for the next generation of numerical software
Symbolics.jl is a high-performance symbolic computation library for the Julia programming language. It enables users to define, manipulate, and analyze mathematical expressions symbolically, with strong support for symbolic differentiation, simplification, equation solving, and code generation. Designed for use in scientific computing, machine learning, and engineering, Symbolics.jl integrates smoothly with Julia’s numerical ecosystem, allowing symbolic expressions to be compiled and... -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data. -
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OpenSpiel
Environments and algorithms for research in general reinforcement
OpenSpiel is a collection of environments and algorithms for research in general reinforcement learning and search/planning in games. OpenSpiel supports n-player (single- and multi- agent) zero-sum, cooperative and general-sum, one-shot and sequential, strictly turn-taking and simultaneous-move, perfect and imperfect information games, as well as traditional multiagent environments such as (partially- and fully- observable) grid worlds and social dilemmas. OpenSpiel also includes tools to... -
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OpenRocket
Model-rocketry aerodynamics and trajectory simulation software
OpenRocket is a free and fully featured simulation software for designing, analyzing, and optimizing model rockets before physical construction and launch. It provides a comprehensive environment where users can assemble rocket components, visualize designs in both 2D and 3D, and simulate flight behavior using accurate aerodynamic and physics models. The software incorporates six-degree-of-freedom flight simulation, allowing it to model real-world dynamics such as stability, drag, thrust, and staging effects. ... -
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Elmer finite element software
Open source finite element software for multiphysical problems
Elmer is a finite element software for numerical solution of partial differential equations and multiphysical problems. It includes models of structural mechanics, fluid dynamics, heat transfer, electromagnetics etc. Elmer home is www.csc.fi/elmer -
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NetworkX
Network analysis in Python
NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. Data structures for graphs, digraphs, and multigraphs. Many standard graph algorithms. Network structure and analysis measures. Generators for classic graphs, random graphs, and synthetic networks. Nodes can be "anything" (e.g., text, images, XML records). Edges can hold arbitrary data (e.g., weights, time-series). Open source 3-clause BSD license. Well tested... -
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CGAL
The Computational Geometry Algorithms Library
CGAL or the Computational Geometry Algorithms Library is a C++ library that gives you easy access to a myriad of efficient and reliable geometric algorithms. These algorithms are useful in a wide range of applications, including computer aided design, robotics, molecular biology, medical imaging, geographic information systems and more. CGAL features a great range of data structures and algorithms, including Voronoi diagrams, cell complexes and polyhedra, triangulations, arrangements of... -
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colleague-skill
Transform a cold separation into a warm Skill
colleague-skill is a specialized agent skill designed to simulate a collaborative teammate within AI-driven workflows, enabling agents to behave more like human colleagues in problem-solving scenarios. The project focuses on enhancing interaction quality by introducing role-based behavior, contextual awareness, and cooperative task execution. It allows agents to provide suggestions, feedback, and alternative approaches, mimicking real-world collaboration dynamics. The system likely... -
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Yampa
Functional Reactive Programming domain-specific language
Yampa is a Functional Reactive Programming (FRP) library for Haskell, specifically designed for modeling hybrid systems that involve both continuous and discrete time behaviors, such as games, simulations, robotics, and reactive systems. Based on the concept of signal functions, Yampa offers a declarative way to model time-varying values and their transformations, making it easier to manage complex time-based logic without resorting to imperative state management. It is grounded in strong... -
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tsfresh
Automatic extraction of relevant features from time series
tsfresh is a python package. It automatically calculates a large number of time series characteristics, the so called features. tsfresh is used to to extract characteristics from time series. Without tsfresh, you would have to calculate all characteristics by hand. With tsfresh this process is automated and all your features can be calculated automatically. Further tsfresh is compatible with pythons pandas and scikit-learn APIs, two important packages for Data Science endeavours in python.... -
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SwiftPamphletApp
SwiftUI + Combine + Swift Concurrency Aysnc/Await Actor + GitHub API
Dai Ming's development brochure, a living development manual. macOS app developed with SwiftUI + Combine + Swift Concurrency Aysnc/Await Actor + GitHub API. Pull the code. Directly compile and generate a manual program without Github function. If you want to use the Github function, you can add your GitHub Access Token to gitHubAccessToken in SwiftPamphletAppConfig.swift. Get the GitHub Access Token at Personal Access Tokens here. Remember to tick repo and user in scope. Both Xcode and macOS... -
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Sandspiel
Creative cellular automata browser game
Sandspiel is an interactive, browser-based cellular automata simulation game that allows users to experiment with physics-like behaviors using simple elements such as sand, water, fire, and plant matter. Built with Rust compiled to WebAssembly and rendered using WebGL, it achieves high-performance simulation directly in the browser without requiring installation. The project focuses on creative exploration, enabling users to draw elements onto a canvas and observe emergent behaviors as they... -
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Arduino FOC
Arduino FOC for BLDC and Stepper motors
We live in very exciting times 😃! BLDC motors are entering the hobby community more and more and many great projects have already emerged leveraging their far superior dynamics and power capabilities. BLDC motors have numerous advantages over regular DC motors but they have one big disadvantage, the complexity of control. Even though it has become relatively easy to design and manufacture PCBs and create our own hardware solutions for driving BLDC motors the proper low-cost solutions are yet... -
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NAMD-Automator
A GUI to automate Workflow for setting up and run NAMD simulations
Welcome to NAMD-Automator, a user-friendly graphical interface designed to simplify the process of Molecular Dynamics (MD) Simulation, by creating configuration files, and automate the simulation with simple form-based tabs. NAMD is one of the widely used software for running these simulations, known for its scalability, speed and efficiency with large molecular systems. However, setting up a typical simulation in NAMD usually requires crafting configuration file for each stage of a Conventional MD Simulation (CMD), such as Minimization, Heating, Equilibration and Production. ... -
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L1B3RT45
Harmless liberation prompts
...The repository gathers creative prompt patterns intended to explore model behavior boundaries, roleplay scenarios, and red-teaming techniques. It is positioned more as a prompt experimentation archive than a traditional software library, emphasizing the study of how instruction phrasing can influence AI outputs. The project reflects the growing interest in prompt security, jailbreak testing, and model alignment research within the AI community. Its materials are often used by researchers and enthusiasts studying robustness, safety, and adversarial prompting dynamics. ... -
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HomeRobot
Mobile manipulation research tools for roboticists
HomeRobot is an open source robotics framework developed by Facebook Research (Meta AI) that provides a complete software stack for mobile manipulation in real-world and simulated environments. Designed for low-cost robots such as the Hello Robot Stretch, HomeRobot enables agents to perceive, navigate, and interact with their surroundings through vision and manipulation. The system focuses on Open Vocabulary Mobile Manipulation (OVMM) — a challenging task in which a robot must explore an...
