markovmodel / msmtools
Tools for estimating and analyzing Markov state models
☆40Updated 2 years ago
Related projects ⓘ
Alternatives and complementary repositories for msmtools
- A python framework to run adaptive Markov state model (MSM) simulation on HPC resources☆18Updated 7 months ago
- How to analyze molecular dynamics data with PyEMMA☆72Updated 5 years ago
- The pytram package is deprecated and no longer supported. We recommend to switch to PyEMMA☆9Updated 8 years ago
- Winter is coming...☆12Updated 5 years ago
- Data visualizations for biomolecular dynamics☆17Updated 6 years ago
- Get access to our MD data files.☆25Updated last year
- Automated omics-scale protein modeling and simulation setup.☆52Updated 3 years ago
- OpenMM plugin to interface with PLUMED☆59Updated last week
- High level API for using machine learning models in OpenMM simulations☆82Updated 3 months 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…☆51Updated 6 months ago
- Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM☆48Updated 7 years ago
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆109Updated 5 years ago
- Modeling molecular ensembles with scalable data structures and parallel computing☆33Updated 2 months ago
- Analyze correlated motions in MD trajectories with only a few lines of Python.☆31Updated 6 years ago
- Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.☆19Updated 3 years ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆63Updated last month
- ☆26Updated 2 years ago
- Python package for generating Markov state models☆18Updated 2 years ago
- Machine learning predictions of bond dissociation energy☆57Updated 2 months ago
- Example to fit parameters and run CG simulations using TorchMD and Schnet☆42Updated 2 years ago
- PyEMMA Jupyter Notebooks☆11Updated 3 years ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆181Updated last year
- Basis sets, estimators and solvers for the variational approach of conformation dynamics. NOTE: the code has been merged with PyEMMA and …☆10Updated 7 years ago
- An open set of tools for automating tasks relating to small molecules☆64Updated 3 years ago
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆33Updated 2 years ago
- Quickly generate, start and analyze benchmarks for molecular dynamics simulations.☆76Updated 2 months ago
- Integrating Molecular Simulation and Experimental Data☆21Updated 3 years ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆42Updated 3 years ago
- Deep learning meets molecular dynamics.☆175Updated 5 years ago