mkuiper / MD_workflow_pyLinks
Molecular dynamics workflow framework in python.
☆12Updated 2 years ago
Alternatives and similar repositories for MD_workflow_py
Users that are interested in MD_workflow_py are comparing it to the libraries listed below
Sorting:
- A stripped-down set of just antechamber, sqm, and tleap.☆31Updated 3 years ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆64Updated 2 years ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆60Updated last year
- Automatic MARTINI parametrization of small organic molecules☆66Updated last week
- Best Practices article intended for LiveCoMS☆41Updated 5 years ago
- Challenge inputs, details, and results for the SAMPL6 series of challenges☆54Updated 3 years ago
- In silico chemical library engine for high-accuracy chemical property prediction☆60Updated last month
- An open set of tools for automating tasks relating to small molecules☆65Updated 3 years ago
- scripts for analyzing molecular dynamics trajectories using VMD☆38Updated 10 years ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆73Updated this week
- Physical validation of molecular simulations☆56Updated 2 months ago
- Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Groma…☆33Updated 6 years ago
- In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes☆32Updated 4 years ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆41Updated last year
- ☆65Updated last year
- Q6 Repository -- EVB, FEP and LIE simulator.☆31Updated last year
- ☆20Updated 4 years ago
- Experimental small molecule hydration free energy dataset☆30Updated 3 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆34Updated last year
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆69Updated 3 weeks ago
- A physical property evaluation toolkit from the Open Forcefield Consortium.☆56Updated this week
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆29Updated last year
- ASH is a Python-based computational chemistry and QM/MM environment, primarily for molecular calculations in the gas phase, explicit sol…☆72Updated this week
- Scripts for assisting in modeling quantitative structure activity relationships from 2D chemical data☆62Updated 3 years ago
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆114Updated 6 years ago
- Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.☆21Updated 3 years ago
- Python script that creates 2D protein-ligand interaction images☆14Updated 7 years ago
- Automated Monte Carlo Conformational Searching with Python☆17Updated 4 years ago
- Quick Reaction Coordinate using Python☆38Updated 11 months ago
- Calculation of water/solvent partition coefficients with Gromacs.☆27Updated 7 months ago