Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
☆28Dec 4, 2024Updated last year
Alternatives and similar repositories for SeparatedTopologies
Users that are interested in SeparatedTopologies are comparing it to the libraries listed below
Sorting:
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆32Jun 3, 2025Updated 8 months ago
- ☆31Jan 26, 2026Updated last month
- 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
- TorchMD-NET. This is a simple code to train Schnet using pytorch-lighthing.☆11Nov 10, 2021Updated 4 years ago
- Lab policies, training, style guides, etc.☆35Dec 9, 2025Updated 2 months ago
- ☆16Dec 24, 2016Updated 9 years ago
- High Information Mapper (HiMap), successor of the Lead Optimization Mapper (LOMAP)☆16May 3, 2023Updated 2 years ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆75Jun 12, 2023Updated 2 years ago
- Python code for generating Boresch restraints from MD simulations☆22Oct 11, 2025Updated 4 months ago
- Package for consistent reporting of relative free energy results☆41Feb 20, 2026Updated last week
- Set up relative free energy calculations using a common scaffold☆24Aug 19, 2025Updated 6 months ago
- ML-based molecular representation models using PyTorch☆16Updated this week
- OpenMM testbed for constant-pH methodologies.☆24Sep 20, 2021Updated 4 years ago
- Absolute solvation free energy calculations with OpenFF and OpenMM☆30Dec 1, 2024Updated last year
- ☆16Jul 28, 2022Updated 3 years ago
- ☆13Jun 11, 2024Updated last year
- Benchmark set for relative free energy calculations.☆119May 22, 2024Updated last year
- Materials for the 2021 PRACE Workshop @ SurfSARA☆30Nov 11, 2021Updated 4 years ago
- This package contains tools for setting up hybrid-topology FE calculations☆38Feb 20, 2026Updated last week
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆220Jan 27, 2026Updated last month
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆72Feb 13, 2026Updated 2 weeks ago
- ChemCharts is a module that allows you to plot chemical space in various figure types☆16Sep 24, 2023Updated 2 years ago
- BLaDE is a Basic Lambda Dynamics Engine for molecular dynamics based alchemical free energy calculations using multisite lambda dynamics …☆18Sep 16, 2025Updated 5 months ago
- OpenFF NAGL☆19Feb 10, 2026Updated 2 weeks ago
- The Open Free Energy toolkit☆253Updated this week
- OpenMM plugin to define forces with neural networks☆32Jan 9, 2020Updated 6 years ago
- A comprehensive toolkit for predicting free energies☆58Jan 10, 2025Updated last year
- ☆41Nov 2, 2024Updated last year
- Chemical perception tree automated exploration tool.☆19Aug 14, 2018Updated 7 years ago
- the simple alchemistry library☆234Jan 23, 2026Updated last month
- A project (and object) for storing, manipulating, and converting molecular mechanics data.☆88Updated this week
- core data models of the Open Free Energy ecosystem☆40Updated this week
- Alchemical mutation scoring map☆41Nov 21, 2025Updated 3 months ago
- ☆69Updated this week
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆193Jul 6, 2023Updated 2 years ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Jul 28, 2022Updated 3 years ago
- Gromacs molecular dynamics simulation analysis scripts☆10Apr 5, 2022Updated 3 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆169Feb 12, 2026Updated 2 weeks ago
- Experiments with expanded ensembles to explore chemical space☆199Oct 28, 2025Updated 4 months ago