A python framework to run adaptive Markov state model (MSM) simulation on HPC resources
☆17Aug 1, 2025Updated last year
Alternatives and similar repositories for adaptivemd
Users that are interested in adaptivemd are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Basis sets, estimators and solvers for the variational approach of conformation dynamics. NOTE: the code has been merged with PyEMMA and …☆10Dec 8, 2016Updated 9 years ago
- Generate Ramachandran plots for single PDB structure and as heatmap for MD trajectory☆11Apr 6, 2022Updated 4 years ago
- Winter is coming...☆14Jan 23, 2019Updated 7 years ago
- conda build recipes for the Omnia project☆24Aug 3, 2021Updated 5 years ago
- Tools for estimating and analyzing Markov state models☆41Aug 15, 2022Updated 4 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- An open source Python framework for transition interface and path sampling calculations.☆118Jun 6, 2026Updated 3 months ago
- IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook☆43Feb 14, 2019Updated 7 years ago
- Molecular dynamics workflow framework in python.☆13Nov 15, 2022Updated 3 years ago
- The pytram package is deprecated and no longer supported. We recommend to switch to PyEMMA☆10May 25, 2016Updated 10 years ago
- 🚂 Python API for Emma's Markov Model Algorithms 🚂☆340Sep 11, 2023Updated 3 years ago
- Datasets for open forcefield parameterization and development☆11Sep 22, 2019Updated 6 years ago
- A plugin that allows the use of Tensorflow in Hoomd-Blue for GPU-accelerated ML+MD☆33Aug 3, 2024Updated 2 years ago
- OpenMM testbed for constant-pH methodologies.☆26Sep 20, 2021Updated 4 years ago
- Coarse-graining library that implements Force-matching☆11Aug 31, 2020Updated 6 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Examples for use of YANK - getyank.org☆12Sep 20, 2021Updated 4 years ago
- Bayesian hidden Markov models toolkit☆48Aug 25, 2020Updated 6 years ago
- PyEMMA Jupyter Notebooks☆13Jan 28, 2021Updated 5 years ago
- pyGPCCA - python GPCCA: Generalized Perron Cluster Cluster Analysis package to coarse-grain reversible and non-reversible Markov state mo…☆30Feb 17, 2026Updated 7 months ago
- ☆11Jun 8, 2018Updated 8 years ago
- Tool collection to integrate and mix OpenEye and OpenMM☆14Jul 17, 2023Updated 3 years ago
- A repository of update in molecular dynamics field by recent progress in machine learning and deep learning.☆345Jan 25, 2026Updated 7 months ago
- Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations☆23Mar 13, 2018Updated 8 years ago
- Automated omics-scale protein modeling and simulation setup.☆53Sep 20, 2021Updated 4 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- ☆32Feb 24, 2022Updated 4 years ago
- Sire Molecular Simulations Framework☆98Jul 17, 2023Updated 3 years ago
- An implementation of SchNet in JAX and JAX-MD.☆17Apr 5, 2022Updated 4 years ago
- Various tutorials about MD setup and analysis, protein-ligand docking, machine learning and lots of other interesting things.☆35Jan 2, 2021Updated 5 years ago
- An open library for the analysis of molecular dynamics trajectories☆735Updated this week
- A tool for setting up free energy simulations.☆37Oct 20, 2022Updated 3 years ago
- How to analyze molecular dynamics data with PyEMMA☆88May 29, 2019Updated 7 years ago
- Graph Inference on MoLEcular Topology☆26Mar 25, 2023Updated 3 years ago
- Molecular dynamics trajectory analysis in Tensorflow☆37Jun 21, 2017Updated 9 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Sampling-based approach to analyse neural networks using TensorFlow☆23Apr 10, 2019Updated 7 years ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆47Sep 29, 2021Updated 4 years ago
- Ensembler is a python package that provides fast and easy access to 1D and 2D model system simulations. It can be used for method develop…☆59May 3, 2024Updated 2 years ago
- ☆20Jun 26, 2020Updated 6 years ago
- A flexible ALPS/Aprun task bundler☆11Mar 26, 2018Updated 8 years ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆203Jul 6, 2023Updated 3 years ago
- Python library to run structure based model (SBM) simulations using the OpenMM toolkit☆25Jan 16, 2026Updated 8 months ago