mkuiper / MD_workflow_py
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
- A stripped-down set of just antechamber, sqm, and tleap.☆30Updated 3 years ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆65Updated last month
- scripts for analyzing molecular dynamics trajectories using VMD☆38Updated 9 years ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆28Updated 11 months ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆36Updated 9 months ago
- Best Practices article intended for LiveCoMS☆37Updated 5 years ago
- ☆64Updated last year
- Q6 Repository -- EVB, FEP and LIE simulator.☆31Updated last year
- How to analyze molecular dynamics data with PyEMMA☆73Updated 5 years ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆57Updated 11 months ago
- Conformer-Rotamer Ensemble Sampling Tool based on the xtb Semiempirical Extended Tight-Binding Program Package☆29Updated this week
- Tools, tutorials, and wiki for GROMACS☆19Updated 4 years ago
- Yasara plugins for Gromacs users☆25Updated last year
- Solvation Structure and Thermodynamic Mapping☆38Updated 9 months 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…☆51Updated 8 months ago
- psi4+RDKit☆98Updated 2 years ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆28Updated 4 years ago
- Quick Reaction Coordinate using Python☆38Updated 6 months ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- ASH is a Python-based computational chemistry and QM/MM environment, primarily for molecular calculations in the gas phase, explicit sol…☆65Updated this week
- Automatic MARTINI parametrization of small organic molecules☆64Updated last month
- Using Gomacs from IPython notebook☆19Updated 10 years ago
- Generate Boltzmann-weighted Sterimol Steric Parameters for Conformationally-Flexible Substituents☆28Updated 2 years ago
- Experimental small molecule hydration free energy dataset☆30Updated 2 years ago
- Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.☆20Updated 3 years ago
- Implementing OPLS-AA/M Force field in OpenMM from CHARMM formatted parameter files☆11Updated 9 years ago
- CAlculation of NMR Chemical Shifts using Deep LEarning☆58Updated last year
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆110Updated 6 years ago
- In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes☆31Updated 4 years ago
- Calculation of water/solvent partition coefficients with Gromacs.☆26Updated 3 months ago