markovmodel / PyEMMA_IPythonLinks
PyEMMA Jupyter Notebooks
☆12Updated 4 years ago
Alternatives and similar repositories for PyEMMA_IPython
Users that are interested in PyEMMA_IPython are comparing it to the libraries listed below
Sorting:
- ☆31Updated 3 years ago
- A python framework to run adaptive Markov state model (MSM) simulation on HPC resources☆18Updated 2 months ago
- A python package for performing GROMACS simulation ensembles☆17Updated 5 months ago
- MDAnalysis tool to calculate membrane curvature.☆32Updated 2 months ago
- Enhanced protein mutational sampling using time-lagged variational autoencoders☆30Updated 7 years ago
- Calculation of water/solvent partition coefficients with Gromacs.☆28Updated 11 months ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆15Updated last week
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes☆33Updated 4 years ago
- Conformer-Rotamer Ensemble Sampling Tool based on the xtb Semiempirical Extended Tight-Binding Program Package☆35Updated 2 months ago
- Helper function for Markov State Models☆12Updated last year
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆23Updated last year
- Coarse-grained mapping and parametrisation for the Martini 3 forcefield☆20Updated 2 months ago
- Using supervised machine learning to build collective variables for accelerated sampling☆28Updated 7 years ago
- scripts for analyzing molecular dynamics trajectories using VMD☆39Updated 10 years ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆25Updated 5 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 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…☆54Updated last year
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 years ago
- Graph-based generative model☆25Updated 6 years ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆41Updated last year
- A database of reaction properties containing the atom-mapped reaction SMILES and the target properties.☆34Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- Using neural networks for enhanced sampling in computational biophysics☆16Updated 8 years ago
- Machine learning predictions of bond dissociation energy☆65Updated last year
- Generate Boltzmann-weighted Sterimol Steric Parameters for Conformationally-Flexible Substituents☆29Updated 3 years ago
- Collection of interaction and molecule parameters for the Martini3 force-field☆19Updated 2 years ago
- Repository for MD methods and analysis from submitted or published work☆19Updated 2 years ago
- Force field-inspired molecular representation learning model☆21Updated 2 years ago
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆15Updated 3 years ago