alchemistry / alchemlyb
the simple alchemistry library
☆208Updated 3 months ago
Alternatives and similar repositories for alchemlyb:
Users that are interested in alchemlyb are comparing it to the libraries listed below
- Force fields produced by the Open Force Field Initiative☆148Updated 3 weeks ago
- Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates☆136Updated 5 months ago
- Describe and apply transformation on molecular structures and topologies☆108Updated this week
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆125Updated 9 months ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆131Updated last month
- Conversion tool for molecular simulations☆194Updated 9 months ago
- Python implementation of the multistate Bennett acceptance ratio (MBAR)☆246Updated 5 months ago
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆263Updated last month
- Experimental and calculated small molecule hydration free energies☆114Updated 2 years ago
- A Python package for calculating molecular features☆169Updated 2 months ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆183Updated last year
- OFFICIAL: AnteChamber PYthon Parser interfacE☆221Updated 2 months ago
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆282Updated 2 weeks ago
- The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avai…☆335Updated this week
- Scoring of shape and ESP similarity with RDKit☆212Updated last year
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆183Updated last year
- An open source Python framework for transition interface and path sampling calculations.☆110Updated 2 months ago
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆113Updated 6 years ago
- Auto3D generates low-energy conformers from SMILES/SDF☆163Updated this week
- Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196☆229Updated 4 months ago
- Calculate quasi-harmonic free energies from Gaussian output files with temperature and other corrections☆142Updated 6 months ago
- Automated Quantum Mechanical Environments (AQME) offers transparent and reproducible workflows available for Jupyter Notebooks and comman…☆104Updated last month
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆141Updated 3 months ago
- Martini 3 small-molecule database☆57Updated 6 months ago
- Benchmark set for relative free energy calculations.☆105Updated 9 months ago
- OpenMM plugin to interface with PLUMED☆66Updated 2 weeks ago
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆189Updated last month
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆137Updated 2 weeks ago
- An interoperable Python framework for biomolecular simulation.☆107Updated this week
- Collective variables library for molecular simulation and analysis programs☆218Updated this week