markovmodel / adaptivemdLinks
A python framework to run adaptive Markov state model (MSM) simulation on HPC resources
☆18Updated 6 months ago
Alternatives and similar repositories for adaptivemd
Users that are interested in adaptivemd are comparing it to the libraries listed below
Sorting:
- ☆32Updated 3 years ago
- Calculation of water/solvent partition coefficients with Gromacs.☆29Updated last year
- Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.☆21Updated 4 years ago
- How to analyze molecular dynamics data with PyEMMA☆82Updated 6 years ago
- Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations☆20Updated 7 years ago
- Package for consistent reporting of relative free energy results☆41Updated last week
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆34Updated 2 months ago
- In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes☆34Updated 5 years ago
- An open set of tools for automating tasks relating to small molecules☆69Updated 4 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…☆55Updated last year
- Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.☆26Updated 4 years ago
- Experimental small molecule hydration free energy dataset☆30Updated 3 years ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆43Updated last year
- A fast solver for large scale MBAR/UWHAM equations☆40Updated last year
- Physical validation of molecular simulations☆57Updated last month
- Dihedral scanner with wavefront propagation☆35Updated 9 months ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆67Updated 2 years ago
- Parallel algorithms for MDAnalysis☆31Updated last year
- Main code repository for FATSLiM☆23Updated 3 years ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆46Updated 4 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 years ago
- Python Tools for NAMD☆23Updated 9 months ago
- Best Practices article intended for LiveCoMS☆42Updated 6 years ago
- A comprehensive toolkit for predicting free energies☆58Updated last year
- Copernicus☆18Updated 8 years ago
- OpenMM plugin to interface with PLUMED☆74Updated 3 weeks ago
- Quickly generate, start and analyze benchmarks for molecular dynamics simulations.☆80Updated last year
- Modeling molecular ensembles with scalable data structures and parallel computing☆36Updated 3 weeks ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆35Updated 2 years ago
- A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format☆31Updated last month