Search Results for "molecular dynamics simulation"

Showing 387 open source projects for "molecular dynamics simulation"

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    FreeCAD

    A free and open source multiplatform 3D parametric modeler

    FreeCAD is an open-source parametric 3D modeler made primarily to design real-life objects of any size. Parametric modeling allows you to easily modify your design by going back into your model history and changing its parameters. FreeCAD allows you to sketch geometry constrained 2D shapes and use them as a base to build other objects. It contains many components to adjust dimensions or extract design details from 3D models to create high quality production ready drawings. FreeCAD is a...
    Downloads: 34 This Week
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    Bullet Physics SDK

    Bullet Physics SDK

    Real-time collision detection and multi-physics simulation for VR

    This is the official C++ source code repository of the Bullet Physics SDK: real-time collision detection and multi-physics simulation for VR, games, visual effects, robotics, machine learning etc. We are developing a new differentiable simulator for robotics learning, called Tiny Differentiable Simulator, or TDS. The simulator allows for hybrid simulation with neural networks. It allows different automatic differentiation backends, for forward and reverse mode gradients. TDS can be trained...
    Downloads: 3 This Week
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  • 3
    Molly.jl

    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. Slides are also available for a tutorial in September...
    Downloads: 0 This Week
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  • 4
    Kinetic.jl

    Kinetic.jl

    Universal modeling and simulation of fluid mechanics upon ML

    Kinetic is a computational fluid dynamics toolbox written in Julia. It aims to furnish efficient modeling and simulation methodologies for fluid dynamics, augmented by the power of machine learning. Based on differentiable programming, mechanical and neural network models are fused and solved in a unified framework. Simultaneous 1-3 dimensional numerical simulations can be performed on CPUs and GPUs.
    Downloads: 0 This Week
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    PowerSimulationsDynamics.jl

    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.
    Downloads: 0 This Week
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  • 6
    OpenFOAM

    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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    Downloads: 2,771 This Week
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  • 7
    vaspkit
    Basic features: 1. Generate KPOINTS, POTCAR and INCAR for a given POSCAR file; 2. Elastic-constants using stress-strain or energy-strain methods; 3. Equation-of-state fitting; 4. Suggested k-paths for a given crystal structure; 5. Optical adsorption coefficient; 6. Band structure unfolding; 7. Fermi surface; 8. Density-of-states and band-structure; 9. Charge/spin density, Charge density difference; 10. Vacuum level and work function; 11. Wave-function analysis; 12. Molecular-dynamics analysis...
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    Downloads: 849 This Week
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  • 8
    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.
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    Downloads: 112 This Week
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  • 9

    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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    Downloads: 204 This Week
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  • 10
    Minsky

    Minsky

    System dynamics program with additional features for economics

    Minsky brings system dynamics and monetary modelling to economics. Models are defined using flowcharts on a drawing canvas (as are Matlab's Simulink, Vensim, Stella, etc). Minsky's unique feature is the "Godley Table", which uses double entry bookkeeping to generate stock-flow consistent models of financial flows. Minsky is good for demonstrating mathematics too, with the most "math-like" interface in system dynamics. Sign up to Minsky's Patreon page (for as little as $1 a month) at https...
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    Downloads: 62 This Week
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  • 11
    CFDTool - MATLAB CFD Simulation GUI Tool

    CFDTool - MATLAB CFD Simulation GUI Tool

    CFDTool - Easy to Use Fluid Dynamics (CFD) MATLAB Toolbox

    CFDTool - An Easy to Use CFD Toolbox for MATLAB ======================================= CFDTool is a MATLAB® Computational Fluid Dynamics (CFD) Toolbox for modeling and simulation of fluid flows with coupled heat transfer. Based on FEATool Multiphysics (https://www.featool.com), CFDTool is specifically designed to make fluid dynamics and heat transfer simulations both easy and enjoyable. - Completely stand-alone and self-contained toolbox - Fully integrated and easy to use Graphical User...
    Downloads: 9 This Week
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  • 12
    RINGS "Rigorous Investigation of Networks Generated using Simulations" is a scientific code developed in Fortran90/MPI to analyze the results of molecular dynamics simulations. Its main feature is the analysis of the connectivity using ring statistics.
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    Downloads: 40 This Week
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  • 13

    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...
    Downloads: 27 This Week
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  • 14
    oxDNA

    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.
    Downloads: 19 This Week
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  • 15
    WavePacket (Matlab/Octave)

    WavePacket (Matlab/Octave)

    Dynamics of quantum systems, controlled by external fields

    WavePacket is a program package for numerical simulation of quantum-mechanical wavepacket dynamics of distinguishable particles. It can be used to solve single or coupled time-independent or time-dependent (linear) Schrödinger and Liouville-von Neumann-equations, partly also classical or quantum-classical Liouville equations. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can be used to simulate modern...
    Downloads: 9 This Week
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  • 16
    OpenDSS-G

    OpenDSS-G

    A graphical view of OpenDSS

    OpenDSS-G (fomer DSSim-PC) is a new step in the evolution of simulation tools for planning and operations based in OpenDSS. This interface has adopted the functionalities of OpenDSS for making easier to the user to use the advance features of the platform. This version includes the parallel processing features included in OpenDSS. The interface is faster and by using graphical objects and forms the user can describe the power system, configure the processor utilization and many more advance...
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    Downloads: 70 This Week
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  • 17
    relax

    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...
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    Downloads: 22 This Week
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  • 18
    vmdStore

    vmdStore

    vmdStore provides a user-friendly interface to free install VMD plugin

    vmdStore provides a user-friendly interface to free install VMD plugins. vmdStore also helps you keeping the plugins always updated. Minimum Requirements Operating System: macOS, Linux, or Windows Visual Molecular Dynamics (VMD) 1.9.3 or later
    Downloads: 23 This Week
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  • 19
    XMD is a program for performing molecular dynamic simulations on metals and some ceramics materials at the atomic scale. It models atomic energies and dynamics using user defined pair potentialsl, EAM potentials and some hard coded potentials.
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    Downloads: 14 This Week
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  • 20

    42

    Simulation for spacecraft attitude control system analysis and design

    42 is a comprehensive general-purpose simulation of spacecraft attitude and orbit dynamics. Its primary purpose is to support design and validation of attitude control systems, from concept studies through integration and test. 42 accurately models multi-body spacecraft attitude dynamics (with rigid and/or flexible bodies), and both two-body and three-body orbital flight regimes, modelling environments from low Earth orbit to throughout the solar system. 42 simulates multiple spacecraft...
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    Downloads: 18 This Week
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  • 21
    MzDOCK - Multiple Ligand Docking Tool

    MzDOCK - Multiple Ligand Docking Tool

    MzDOCK is A Virtual Screening Tool For Drug Discovery Research

    - Molecular Docking Virtual Screening Tool To Aid In Drug Discovery Research. - Developed with Synchronized functioning of Python and Batch scripts - Compatible on Windows
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    Downloads: 11 This Week
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  • 22

    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. Detailed description of model can be found in Y.K.Batygin, “Particle-in-cell code BEAMPATH for beam dynamics...
    Downloads: 10 This Week
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  • 23

    MD Log parser

    Standalone application for parsing MD simulation Log files

    The MD Log Parser project focuses on creating a tool designed to parse log files from molecular dynamics (MD) simulations and generate informative graphs. Log files from MD simulations contain crucial details regarding the simulation's progression, energy terms, trajectories, and other pertinent parameters. Extracting and comprehensively analyzing this data manually can be both time-intensive and demanding. Consequently, the MD Log Parser project seeks to automate this procedure, offering...
    Downloads: 0 This Week
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  • 24

    ERmod

    Approximate solvation free energy calculator

    ERmod (Energy Representation Module) is a program to calculate the solvation free energy based on the energy representation method (J. Chem. Phys. 113, 6070 (2000)). The program allows users to calculate the solvation free energy to arbitrary solvents, including inhomogeneous systems, and can run in cooperation with state-of-art molecular simulation softwares, such as NAMD, GROMACS and/or AMBER.
    Downloads: 13 This Week
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  • 25
    GroIMP

    GroIMP

    Growth-grammar related Interactive Modelling Platform

    ... integrated, e.g., the user can interactively select the rules to be applied. GroIMP provides classes that can be used in modelling: Turtle commands, further geometrical classes like bicubic surfaces, the class Cell which has been used in the Game Of Life implementation, and so on. The outcome of a model is visualised within GroIMP. In the visual representation of the model output, users can interact with the dynamics of the model, e.g., by selecting or deleting elements.
    Downloads: 8 This Week
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