Search Results for "molecular dynamics simulation"
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Showing 408 open source projects for "molecular dynamics simulation"
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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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WaterLily.jl
Fast and simple fluid simulator in Julia
WaterLily.jl is a fluid dynamics simulation package in Julia that uses lattice Boltzmann methods (LBM) to simulate incompressible flows and fluid-structure interactions in two dimensions. It is designed for easy use and rapid prototyping of physical systems involving particles, obstacles, and hydrodynamic forces. The package is well-suited for educational purposes, computational physics research, and lightweight fluid simulations. -
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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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BioNeMo
BioNeMo Framework: For building and adapting AI models
BioNeMo is an AI-powered framework developed by NVIDIA for protein and molecular generation using deep learning models. It provides researchers and developers with tools to design, analyze, and optimize biological molecules, aiding in drug discovery and synthetic biology applications. -
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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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Flexe
The open source federated learning for vehicular network simulation
Flexe is a FL simulator designed for connected and autonomous vehicles (CAVs). It enables horizontal/vertical/transfer FL schemes and simulates realistic wireless and vehicular dynamics. Separate Python client (PyFlexe) available. -
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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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Planck.js
2D JavaScript Physics Engine
Planck.js is a JavaScript rewrite/port of the physics engine Box2D, designed to provide 2D rigid-body physics simulation usable directly in web contexts or any JavaScript environment. By offering collision detection, rigid-body dynamics, joints, and simulation capabilities, Planck.js makes it possible for developers to build physically realistic 2D games, simulations, or visualizations in browsers or Node.js without relying on native code. Its API mirrors Box2D’s concepts — bodies, fixtures, shapes, joints — which makes it familiar to users of classic Box2D, while being idiomatic for JavaScript developers. ... -
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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 and many other simulation environments. -
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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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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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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... -
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PowerSimulationsDynamics.jl
Julia package to run Dynamic Power System simulations
PowerSimulationsDynamics.jl is a Julia package for power system modeling and simulation of Power Systems dynamics. -
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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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Diffusion for World Modeling
Learning agent trained in a diffusion world model
Diffusion for World Modeling is an experimental reinforcement learning system that trains intelligent agents inside a simulated environment generated by a diffusion-based world model. The project introduces the idea of using diffusion models, commonly used for image generation, to simulate the dynamics of an environment and predict future states based on previous observations and actions. Instead of interacting directly with a real environment, the reinforcement learning agent learns within... -
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foam-extend
Open Source CFD Toolbox
The foam-extend project is a fork of the OpenFOAM® open source library for Computational Fluid Dynamics (CFD). The goal of this project is to integrate community contributions to the foam-extend CFD simulation toolbox. It is an open project welcoming and integrating contributions from all users and developers. -
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MuJoCo
Multi-Joint dynamics with Contact. A general purpose physics simulator
MuJoCo, developed and maintained by Google DeepMind, is a high-performance physics engine designed for simulating complex, articulated systems that interact through contact. It is widely used in research fields such as robotics, biomechanics, computer graphics, animation, and machine learning, where fast and accurate physics simulations are essential. The engine provides a robust C API optimized for real-time computation, making it suitable for scientific research and advanced simulation... -
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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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oxDNA
A code primarily aimed at DNA and RNA coarse-grained simulations
The oxDNA code has been moved to https://github.com/lorenzo-rovigatti/oxDNA, please go there for new releases. -
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OpenFOAM
The Open Source CFD Toolbox
OpenFOAM - The Open Source CFD Toolbox. OpenFOAM is a generic, programmable software tool for Computational Fluid Dynamics (CFD). For more information, see: - Main Website: https://openfoam.org - C++ Source Documentation: https://cpp.openfoam.org - Issue (Bug) Tracking: https://bugs.openfoam.org - User Guide: https://cfd.direct/openfoam/user-guide -
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CFDTool - CFD & OpenFOAM GUI Toolbox
CFDTool - Easy to Use Computational Fluid Dynamics (CFD) Toolbox
CFDTool - "CFD Simulation Made Easy" CFDTool is a fluid dynamics toolbox for modeling and simulation of flows with coupled heat transfer. Based on FEATool Multiphysics (https://www.featool.com), CFDTool is specifically designed to make advanced fluid mechanics and heat transfer simulations both easy and enjoyable. - Completely stand-alone and cross-platform self-contained toolbox - Optionally use as MATLAB Add-On toolbox - Fully integrated and easy to use MATLAB GUI - Modeling and simulation in 1D, 2D, 3D, and axisymmetric/swirl/cylindrical coordinate systems - Seamless OpenFOAM GUI and SU2 CFD solver integrations (https://www.featool.com/Easy-to-Use-OpenFOAM-GUI) - Built-in geometry and CAD tools - Automatic mesh and grid generation - Pre-defined equations and boundary conditions for: + Incompressible viscous fluid flows (Navier-Stokes equations) + Compressible, supersonic, trans-sonic, and turbulent flows + Heat conduction with conjugate heat transfer -
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VectorizedMultiAgentSimulator (VMAS)
VMAS is a vectorized differentiable simulator
VectorizedMultiAgentSimulator is a high-performance, vectorized simulator for multi-agent systems, focusing on large-scale agent interactions in shared environments. It is designed for research in multi-agent reinforcement learning, robotics, and autonomous systems where thousands of agents need to be simulated efficiently. -
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Beampath
Beam dynamics simulations in linear accelerators and beamlines
BEAMPATH is a 2D and 3D code for simulation of space charge dominated beam dynamics in linear particle accelerators and beam transport. The program is used for particle-in-cell simulation of axial-symmetric, quadrupole-symmetric and z-uniform beams in a channel containing RF gaps, radio-frequency quadrupoles, multipole lenses, solenoids, bending magnets, accelerating waveguides. -
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SpikingJelly
SpikingJelly is an open-source deep learning framework
SpikingJelly is an open-source deep learning framework for spiking neural networks that is primarily built on top of PyTorch and aimed at neuromorphic computing research. The project provides the components needed to build, train, and evaluate neural models that communicate through discrete spikes rather than the continuous activations used in conventional artificial neural networks. This makes it especially relevant for researchers interested in biologically inspired computing, event-driven... -
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The goal of this project is to open the OpenFOAM CFD toolbox to community contributed extensions. Visit https://sourceforge.net/p/openfoam-extend/wiki/Home/ for more information. OPENFOAM(R) is a registered trademark of OpenCFD Limited.
