PyEMMA Jupyter Notebooks
☆13Jan 28, 2021Updated 5 years ago
Alternatives and similar repositories for PyEMMA_IPython
Users that are interested in PyEMMA_IPython are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Winter is coming...☆14Jan 23, 2019Updated 7 years ago
- The pytram package is deprecated and no longer supported. We recommend to switch to PyEMMA☆10May 25, 2016Updated 9 years ago
- Tools for estimating and analyzing Markov state models☆41Aug 15, 2022Updated 3 years ago
- A VMD script to calculate side-chain and backbone dihedrals (torsion angles)☆14Jun 4, 2016Updated 9 years ago
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆24Jun 8, 2024Updated last year
- 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.
- Cryptic pocket prediction using AlphaFold 2☆25Nov 27, 2022Updated 3 years ago
- C++ implementation of the Diffusion Map, with Python bindings☆10Aug 22, 2017Updated 8 years ago
- Example files for Colvars module: https://github.com/Colvars/colvars☆13Dec 7, 2021Updated 4 years ago
- Learning free energy landscapes using artificial neural networks☆14Nov 30, 2017Updated 8 years ago
- Demo of diffusion models #DDPM applied to molecular dynamics of small peptide☆14Jan 26, 2024Updated 2 years ago
- Python Tools for NAMD☆24May 7, 2025Updated 11 months ago
- Generate Ramachandran plots for single PDB structure and as heatmap for MD trajectory☆11Apr 6, 2022Updated 4 years ago
- Tutorials on doing AMBER based Metadynamics and Gaussian Accelerated MD (GaMD)☆12Dec 1, 2025Updated 4 months ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Mar 7, 2025Updated last year
- NordVPN Special Discount Offer • AdSave on top-rated NordVPN 1 or 2-year plans with secure browsing, privacy protection, and support for for all major platforms.
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Mar 30, 2026Updated last week
- 🚂 Python API for Emma's Markov Model Algorithms 🚂☆339Sep 11, 2023Updated 2 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆48Feb 11, 2021Updated 5 years ago
- Computation of the drug-target relative residence times from RAMD simulations☆21Aug 29, 2024Updated last year
- A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling metho…☆23Sep 26, 2024Updated last year
- A python framework to run adaptive Markov state model (MSM) simulation on HPC resources☆17Aug 1, 2025Updated 8 months ago
- Automatic CHARMM-GUI browser interaction with Python☆18Mar 20, 2023Updated 3 years ago
- Repository of the data for PLUMED Masterclass 22.3☆14Jul 10, 2024Updated last year
- Tutorial to build AMBER compatable protein+lipid systems☆16Apr 19, 2017Updated 8 years ago
- NordVPN Special Discount Offer • AdSave on top-rated NordVPN 1 or 2-year plans with secure browsing, privacy protection, and support for for all major platforms.
- Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.☆17Mar 30, 2026Updated last week
- Robust and stable clustering of molecular dynamics simulation trajectories.☆19Sep 2, 2022Updated 3 years ago
- PiViewer: an open-source tool for automated detection and display of pi-pi interactions☆14Jun 6, 2018Updated 7 years ago
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Mar 2, 2026Updated last month
- 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
- ☆21Dec 11, 2024Updated last year
- Accelerating Metadynamics-Based Free-Energy Calculations with Adaptive Machine Learning Potentials☆17Jun 9, 2021Updated 4 years ago
- Python utility functions for the analysis of diffusion in molecular dynamics simulation trajectories.☆18Jun 21, 2022Updated 3 years ago
- ☆71Jul 19, 2023Updated 2 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.
- Julia utilities for reading in and analyzing Gromacs simulation results☆17Oct 3, 2020Updated 5 years ago
- How to analyze molecular dynamics data with PyEMMA☆85May 29, 2019Updated 6 years ago
- The gmx_rrcs script is designed to calculate the residues-residues contact scores (rrcs) from a trajectory file generated by GROMACS.☆18Jun 16, 2025Updated 9 months ago
- Main repository for METAGUI3☆20Jun 19, 2021Updated 4 years ago
- For the purpose of post progressing of MD carried by gromacs☆23Jul 2, 2025Updated 9 months ago
- ☆32Sep 23, 2023Updated 2 years ago
- A computation graph micro-framework providing seamless lazy and concurrent evaluation☆16Feb 14, 2020Updated 6 years ago