choderalab / pymbarLinks
Python implementation of the multistate Bennett acceptance ratio (MBAR)
☆288Updated 3 months ago
Alternatives and similar repositories for pymbar
Users that are interested in pymbar are comparing it to the libraries listed below
Sorting:
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆312Updated last week
- The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avai…☆376Updated last week
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆192Updated 2 years ago
- the simple alchemistry library☆232Updated last month
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆343Updated last week
- ANI-1 neural net potential with python interface (ASE)☆225Updated last year
- Force fields produced by the Open Force Field Initiative☆174Updated last week
- Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196☆258Updated 7 months ago
- WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis☆209Updated this week
- Converts an xyz file to an RDKit mol object☆290Updated 11 months ago
- OpenMM plugin to define forces with neural networks☆220Updated 10 months ago
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆134Updated last year
- Collective variables library for molecular simulation and analysis programs☆237Updated this week
- Conversion tool for molecular simulations☆217Updated this week
- An open source Python framework for transition interface and path sampling calculations.☆116Updated last month
- Experiments with expanded ensembles to explore chemical space☆198Updated 2 months ago
- GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).☆184Updated 4 months ago
- OpenMM tutorial for the MSBS course☆182Updated this week
- Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates☆181Updated last month
- Experimental and calculated small molecule hydration free energies☆130Updated 3 years ago
- automated reaction profile generation☆194Updated 2 months ago
- Python-centric Cookiecutter for Molecular Computational Chemistry Packages☆443Updated last month
- High level API for using machine learning models in OpenMM simulations☆139Updated last week
- Describe and apply transformation on molecular structures and topologies☆133Updated this week
- OFFICIAL: AnteChamber PYthon Parser interfacE☆244Updated 7 months ago
- Biomolecular simulation trajectory/data analysis.☆162Updated last month
- Systematic force field optimization.☆156Updated last year
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆117Updated 7 years ago
- molSimplify code☆206Updated last month
- Visual Interactive Analysis of Molecular Dynamics☆315Updated this week