Search Results for "molecular dynamics software"
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Showing 75 open source projects for "molecular dynamics software"
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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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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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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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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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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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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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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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CAMPARI
Software for molecular simulations and trajectory analysis
...Naturally, CAMPARI continues to provide the reference implementation of the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte Carlo and molecular dynamics in seamless fashion. CAMPARI offers the user a very high level of control over all implemented features. For more information and features, please refer to the project's homepage at http://campari.sourceforge.net/V5 -
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PyRx - Virtual Screening Tool
Virtual Screening software for Computational Drug Discovery
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes... -
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GromacsProSuite
Graphical User Interface for Gromacs
This tool is an integrated graphical interface that simplifies molecular dynamics simulations using Gromacs. It provides a structured, tab-based environment to set up, execute, and analyze simulations data without complex command-line operations. The software automates tasks such as topology generation, solvation, ion addition, minimization, equilibration, and production runs while executing GROMACS commands in the background. -
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ERmod
Approximate solvation free energy calculator
...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 software, such as LAMMPS, GROMACS and/or AMBER. -
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BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
BioXTAS RAW is a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF as well as electron density reconstructions using DENSS. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis (EFA) or the regularized alternating least squares (REGALS) methods. ... -
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
...Contact us - kabeermuzammil614@gmail.com MzDOCK Development - Available on WindowsOS and Linux ubuntu 22.04 and more - Software Authorship - Muzammil Kabier -
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Transformers4Rec
Transformers4Rec is a flexible and efficient library
Transformers4Rec is an advanced recommendation system library that leverages Transformer models for sequential and session-based recommendations. The library works as a bridge between natural language processing (NLP) and recommender systems (RecSys) by integrating with one of the most popular NLP frameworks, Hugging Face Transformers (HF). Transformers4Rec makes state-of-the-art transformer architectures available for RecSys researchers and industry practitioners. Traditional recommendation... -
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PoseidonQ - AI/ML Based QSAR Modeling
ML based QSAR Modelling And Translation of Model to Deployable WebApps
- This Software was made with an intention to make QSAR/QSPR development more efficient and reproducible. - Published in ACS, Journal of Chemical Information and Modeling . Link : https://pubs.acs.org/doi/10.1021/acs.jcim.4c02372 - Simple to use and no compromise on essential features necessary to make reliable QSAR models. - From Generating Reliable ML Based QSAR Models to Developing Your Own QSAR WebApp. For any feedback or queries, contact kabeermuzammil614@gmail.com - Available on... -
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Neural Tangents
Fast and Easy Infinite Neural Networks in Python
Neural Tangents is a high-level neural network API for specifying complex, hierarchical models at both finite and infinite width, built in Python on top of JAX and XLA. It lets researchers define architectures from familiar building blocks—convolutions, pooling, residual connections, and nonlinearities—and obtain not only the finite network but also the corresponding Gaussian Process (GP) kernel of its infinite-width limit. With a single specification, you can compute NNGP and NTK kernels,... -
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SAVA
A Signal Acquisition, Visualization & Analysis software
A Signal Acquisition, Visualization & Analysis software application: * Signals, as in analog sensor data * Acquisition, as in data sampling/capturing/recording * Visualization, as in plotting raw/processed data * Analysis, as in live/post data processing Capabilities: The software has build in support for National Instruments Daq equipment (NI-DAQ) or it can load external source scripts (python), for customizable data sources. -
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towhee
Framework that is dedicated to making neural data processing
Towhee is an open-source machine-learning pipeline that helps you encode your unstructured data into embeddings. You can use our Python API to build a prototype of your pipeline and use Towhee to automatically optimize it for production-ready environments. From images to text to 3D molecular structures, Towhee supports data transformation for nearly 20 different unstructured data modalities. We provide end-to-end pipeline optimizations, covering everything from data decoding/encoding, to... -
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ED Software project contains several programs used (mostly) for processing gas-phase electron diffraction (GED) experimental data.
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capd
Computer Assisted Proofs in Dynamics
Dynamical Systems and Homology Software. The CAPD library is a collection of flexible C++ modules which are mainly designed to computation of homology of sets and maps and nonrigorous and validated numerics for dynamical systems. -
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DockStream
A Docking Wrapper to Enhance De Novo Molecular Design
DockStream is a docking wrapper providing access to a collection of ligand embedders and docking backends. Docking execution and post hoc analysis can be automated via the benchmarking and analysis workflow. The flexilibity to specifiy a large variety of docking configurations allows tailored protocols for diverse end applications. DockStream can also parallelize docking across CPU cores, increasing throughput. DockStream is integrated with the de novo design platform, REINVENT, allowing one... -
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LP CSIC/UAB Apps and Code
Software and Code from Laboratori de Proteòmica CSIC/UAB
Software, Code and Documents from Laboratori de Proteòmica CSIC/UAB ( LP-CSIC/UAB: http://proteomica.uab.cat ) -
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VolFEM3D
VolFem is an open software package for CFD.
VolFem is an open software package for fluid dynamics simulation based on a semi-implicit hybrid finite volume/finite element method. -
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Makani
Makani was developed a commercial-scale airborne wind turbine
...Built primarily in C++ and Python, the codebase integrates real-time flight control, sensor fusion, aerodynamic modeling, and telemetry visualization. The project also provides comprehensive simulation environments for studying airborne wind power systems and flight dynamics. Although Makani’s commercial development concluded, the software remains valuable for researchers and engineers. -
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APBS
Biomolecular electrostatics software
This software has moved to http://www.poissonboltzmann.org/.
