This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
☆34Jun 3, 2025Updated last year
Alternatives and similar repositories for reeds
Users that are interested in reeds are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Tautomer ratios in solution☆28Sep 20, 2021Updated 4 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆29Dec 4, 2024Updated last year
- Set up relative free energy calculations using a common scaffold☆24Apr 21, 2026Updated 3 months ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Oct 27, 2022Updated 3 years ago
- ☆31Jul 8, 2026Updated last month
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- md++ code☆14Updated this week
- the simple alchemistry library☆242Jun 1, 2026Updated 2 months ago
- ☆16Dec 24, 2016Updated 9 years ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆65Dec 17, 2025Updated 7 months ago
- This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and an…☆17Oct 17, 2023Updated 2 years ago
- Code and resources for the EPSRC BioSimSpace project.☆78Sep 1, 2025Updated 11 months ago
- Experiments with expanded ensembles to explore chemical space☆203Oct 28, 2025Updated 9 months ago
- Alchemical mutation scoring map☆42Apr 7, 2022Updated 4 years ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆203Jul 6, 2023Updated 3 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Absolute solvation free energy calculations with OpenFF and OpenMM☆34Dec 1, 2024Updated last year
- Best practice document for alchemical free energy calculations going to livecoms journal☆90May 28, 2026Updated 2 months ago
- Lab policies, training, style guides, etc.☆35Jul 25, 2026Updated 2 weeks ago
- Alchemical mutation scoring map☆45Aug 3, 2026Updated last week
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆173Aug 2, 2026Updated last week
- Python code for generating Boresch restraints from MD simulations☆23Oct 11, 2025Updated 10 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…☆59May 3, 2024Updated 2 years ago
- ☆25Oct 30, 2020Updated 5 years ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆75Jun 12, 2023Updated 3 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- TorchMD-NET. This is a simple code to train Schnet using pytorch-lighthing.☆11Nov 10, 2021Updated 4 years ago
- This package contains tools for setting up hybrid-topology FE calculations☆38Aug 6, 2026Updated last week
- ☆90Jul 19, 2023Updated 3 years ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆16Apr 3, 2026Updated 4 months ago
- Computational Chemistry Workflows☆57Jul 19, 2022Updated 4 years ago
- This repository is the used for teaching the Physical Chemistry Practicum about Molecular Dynamics (MD) simulations for pharmacy and biol…☆12May 7, 2025Updated last year
- Bayesian Multistate Bennett Acceptance Ratio Method☆16Jun 28, 2026Updated last month
- Structure-informed machine learning for kinase modeling☆60Updated this week
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆225Mar 4, 2026Updated 5 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆102Updated this week
- A project (and object) for storing, manipulating, and converting molecular mechanics data.☆95Updated this week
- ☆17Feb 8, 2024Updated 2 years ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆82Jul 6, 2026Updated last month
- A package to identify matched molecular pairs and use them to predict property changes.☆24Apr 30, 2024Updated 2 years ago
- Collection of scripts / notebooks to reliably select datasets☆31Jan 28, 2024Updated 2 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Apr 7, 2022Updated 4 years ago