How to analyze molecular dynamics data with PyEMMA
☆85May 29, 2019Updated 6 years ago
Alternatives and similar repositories for pyemma_tutorials
Users that are interested in pyemma_tutorials are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- 🚂 Python API for Emma's Markov Model Algorithms 🚂☆339Sep 11, 2023Updated 2 years ago
- ☆32Feb 24, 2022Updated 4 years ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆31Dec 19, 2021Updated 4 years ago
- Get access to our MD data files.☆31Nov 22, 2023Updated 2 years ago
- Deep learning meets molecular dynamics.☆188May 3, 2019Updated 6 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting with the flexibility to host WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Cloudways by DigitalOcean.
- An open library for the analysis of molecular dynamics trajectories☆707Mar 31, 2026Updated last week
- Winter is coming...☆14Jan 23, 2019Updated 7 years ago
- Analyze correlated motions in MD trajectories with only a few lines of Python.☆33Jan 17, 2018Updated 8 years ago
- A repository of update in molecular dynamics field by recent progress in machine learning and deep learning.☆335Jan 25, 2026Updated 2 months ago
- Predict allosteric pockets on proteins☆15Mar 28, 2022Updated 4 years ago
- clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)☆127Apr 25, 2024Updated last year
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆118Dec 29, 2018Updated 7 years ago
- PyEMMA Jupyter Notebooks☆13Jan 28, 2021Updated 5 years ago
- A primer on software development best practices for computational chemistry☆274Dec 5, 2022Updated 3 years ago
- 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.
- Using supervised machine learning to build collective variables for accelerated sampling☆28Jun 26, 2018Updated 7 years ago
- A Python package to generate free energy landscape (FEL) of molecular dynamics (MD) trajectory obtained from GROMACS. It also extracts th…☆14Apr 4, 2025Updated last year
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆97Jul 16, 2025Updated 8 months ago
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆16Jul 2, 2024Updated last year
- The Molecular Dynamics teaching code.☆12Oct 17, 2025Updated 5 months ago
- A Python toolkit for the analyis of lipid membrane simulations☆34Oct 24, 2025Updated 5 months ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 7 years ago
- MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store☆31Dec 16, 2023Updated 2 years ago
- Main repository for METAGUI3☆20Jun 19, 2021Updated 4 years ago
- NordVPN Threat Protection Pro™ • AdTake your cybersecurity to the next level. Block phishing, malware, trackers, and ads. Lightweight app that works with all browsers.
- pyGPCCA - python GPCCA: Generalized Perron Cluster Cluster Analysis package to coarse-grain reversible and non-reversible Markov state mo…☆27Feb 17, 2026Updated last month
- IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook☆48Feb 14, 2019Updated 7 years ago
- A python framework to run adaptive Markov state model (MSM) simulation on HPC resources☆17Aug 1, 2025Updated 8 months ago
- Variational Autoencoder for Dimensionality Reduction of Time-Series☆190May 1, 2022Updated 3 years ago
- PDBFixer fixes problems in PDB files☆637Mar 10, 2026Updated 3 weeks ago
- rid☆25Aug 15, 2021Updated 4 years ago
- ☆14Jun 4, 2024Updated last year
- The GB99dms implicit solvent force field for proteins, plus scripts and data☆27Sep 19, 2025Updated 6 months ago
- Statistical models for biomolecular dynamics☆163Jan 26, 2021Updated 5 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting with the flexibility to host WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Cloudways by DigitalOcean.
- Python library for analysis of time series data including dimensionality reduction, clustering, and Markov model estimation☆849Mar 30, 2026Updated last week
- Supporting data for the manuscript "Deep learning the slow modes for rare events sampling"☆21Jun 6, 2024Updated last year
- MDToolbox.jl: A Julia package for molecular dynamics trajectories analysis and modeling of biomolecules☆22Mar 21, 2025Updated last year
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.☆345Mar 21, 2026Updated 2 weeks ago
- GraphVAMPnets combines graph neural networks with variational approach for Markovian process (VAMP) theory to identify the slow collectiv…☆12Feb 20, 2024Updated 2 years ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆201Jul 6, 2023Updated 2 years ago
- GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).☆188Sep 4, 2025Updated 7 months ago