How to analyze molecular dynamics data with PyEMMA
β84May 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
Sorting:
- π Python API for Emma's Markov Model Algorithms πβ339Sep 11, 2023Updated 2 years ago
- β32Feb 24, 2022Updated 4 years ago
- Get access to our MD data files.β31Nov 22, 2023Updated 2 years ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocolβ31Dec 19, 2021Updated 4 years ago
- Deep learning meets molecular dynamics.β186May 3, 2019Updated 6 years ago
- An open library for the analysis of molecular dynamics trajectoriesβ705Mar 12, 2026Updated last week
- Winter is coming...β14Jan 23, 2019Updated 7 years ago
- Analyze correlated motions in MD trajectories with only a few lines of Python.β33Jan 17, 2018Updated 8 years ago
- A repository of update in molecular dynamics field by recent progress in machine learning and deep learning.β334Jan 25, 2026Updated last month
- clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)β128Apr 25, 2024Updated last year
- Predict allosteric pockets on proteinsβ15Mar 28, 2022Updated 3 years ago
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations β¦β118Dec 29, 2018Updated 7 years ago
- PyEMMA Jupyter Notebooksβ14Jan 28, 2021Updated 5 years ago
- A primer on software development best practices for computational chemistryβ274Dec 5, 2022Updated 3 years ago
- Using supervised machine learning to build collective variables for accelerated samplingβ28Jun 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 thβ¦β14Apr 4, 2025Updated 11 months ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calculaβ¦β95Jul 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 apprβ¦β16Jul 2, 2024Updated last year
- The Molecular Dynamics teaching code.β12Oct 17, 2025Updated 5 months ago
- A Python toolkit for the analyis of lipid membrane simulationsβ34Oct 24, 2025Updated 4 months ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)β13Mar 18, 2019Updated 7 years ago
- MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Storeβ31Dec 16, 2023Updated 2 years ago
- Main repository for METAGUI3β20Jun 19, 2021Updated 4 years ago
- pyGPCCA - python GPCCA: Generalized Perron Cluster Cluster Analysis package to coarse-grain reversible and non-reversible Markov state moβ¦β26Feb 17, 2026Updated last month
- PDBFixer fixes problems in PDB filesβ631Mar 10, 2026Updated last week
- A python framework to run adaptive Markov state model (MSM) simulation on HPC resourcesβ18Aug 1, 2025Updated 7 months ago
- IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebookβ49Feb 14, 2019Updated 7 years ago
- ridβ23Aug 15, 2021Updated 4 years ago
- Variational Autoencoder for Dimensionality Reduction of Time-Seriesβ190May 1, 2022Updated 3 years ago
- β14Jun 4, 2024Updated last year
- The GB99dms implicit solvent force field for proteins, plus scripts and dataβ27Sep 19, 2025Updated 6 months ago
- Statistical models for biomolecular dynamicsβ161Jan 26, 2021Updated 5 years ago
- Python library for analysis of time series data including dimensionality reduction, clustering, and Markov model estimationβ846Apr 11, 2025Updated 11 months ago
- Supporting data for the manuscript "Deep learning the slow modes for rare events sampling"β21Jun 6, 2024Updated last year
- MDToolbox.jl: A Julia package for molecular dynamics trajectories analysis and modeling of biomoleculesβ21Mar 21, 2025Updated 11 months ago
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.β339Feb 25, 2026Updated 3 weeks ago
- GraphVAMPnets combines graph neural networks with variational approach for Markovian process (VAMP) theory to identify the slow collectivβ¦β12Feb 20, 2024Updated 2 years ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.β200Jul 6, 2023Updated 2 years ago
- GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).β187Sep 4, 2025Updated 6 months ago