markovmodel / pyemma_tutorials
How to analyze molecular dynamics data with PyEMMA
☆75Updated 5 years ago
Alternatives and similar repositories for pyemma_tutorials:
Users that are interested in pyemma_tutorials are comparing it to the libraries listed below
- A python framework to run adaptive Markov state model (MSM) simulation on HPC resources☆18Updated last year
- Physical validation of molecular simulations☆56Updated 3 weeks ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆63Updated 2 years ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆43Updated 3 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…☆53Updated last year
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆114Updated 6 years ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆58Updated last year
- Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.☆21Updated 3 years ago
- A stripped-down set of just antechamber, sqm, and tleap.☆31Updated 3 years ago
- OpenMM plugin to interface with PLUMED☆66Updated 2 months ago
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆33Updated 3 weeks ago
- An open source Python framework for transition interface and path sampling calculations.☆110Updated 3 months ago
- Quickly generate, start and analyze benchmarks for molecular dynamics simulations.☆79Updated 8 months ago
- High level API for using machine learning models in OpenMM simulations☆104Updated last month
- Package for consistent reporting of relative free energy results☆39Updated last week
- A Python toolkit for the analyis of lipid membrane simulations☆30Updated last month
- Experimental small molecule hydration free energy dataset☆30Updated 3 years ago
- ☆58Updated last month
- Get access to our MD data files.☆28Updated last year
- A fast solver for large scale MBAR/UWHAM equations☆39Updated 8 months ago
- A comprehensive toolkit for predicting free energies☆52Updated 3 months ago
- Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations☆20Updated 7 years ago
- An open set of tools for automating tasks relating to small molecules☆65Updated 3 years ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆67Updated last year
- Experimental and calculated small molecule hydration free energies☆116Updated 2 years ago
- learning coarse-grained force fields☆61Updated 3 years ago
- Parallel algorithms for MDAnalysis☆31Updated 9 months ago
- A physical property evaluation toolkit from the Open Forcefield Consortium.☆56Updated this week
- ☆19Updated 4 years ago
- Best Practices article intended for LiveCoMS☆40Updated 5 years ago