markovmodel / adaptivemd
A python framework to run adaptive Markov state model (MSM) simulation on HPC resources
☆18Updated 11 months ago
Alternatives and similar repositories for adaptivemd:
Users that are interested in adaptivemd are comparing it to the libraries listed below
- How to analyze molecular dynamics data with PyEMMA☆74Updated 5 years ago
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆33Updated 2 years ago
- Package for consistent reporting of relative free energy results☆38Updated 2 months ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆43Updated 3 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 2 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…☆52Updated 10 months ago
- ☆31Updated 3 years ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆37Updated 11 months ago
- In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes☆32Updated 4 years ago
- ☆43Updated 3 years ago
- Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.☆20Updated 3 years ago
- Alchemical tools for OpenMM☆9Updated 3 years ago
- A physical property evaluation toolkit from the Open Forcefield Consortium.☆56Updated this week
- Calculation of water/solvent partition coefficients with Gromacs.☆26Updated 5 months ago
- Experimental small molecule hydration free energy dataset☆30Updated 2 years ago
- Chemical perception tree automated exploration tool.☆19Updated 6 years ago
- OpenMM plugin to interface with PLUMED☆66Updated 3 weeks ago
- Modeling molecular ensembles with scalable data structures and parallel computing☆34Updated last month
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆31Updated 5 years ago
- ☆19Updated 4 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆31Updated last year
- Challenge details, inputs, and results for the SAMPL7 series of challenges☆46Updated 3 years ago
- Physical validation of molecular simulations☆56Updated 2 months ago
- ☆33Updated 6 months ago
- A primer on statistical mechanics for biochemists☆46Updated 2 years ago
- A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format☆28Updated 6 months ago
- Structure-informed machine learning for kinase modeling☆53Updated this week
- A comprehensive toolkit for predicting free energies☆51Updated 2 months ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆28Updated last year
- mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data☆32Updated last week