Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.
☆15Jan 3, 2026Updated 9 months ago
Alternatives and similar repositories for funnel_maker
Users that are interested in funnel_maker are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 7 years ago
- A script for analysing well tempered metadynamics☆11Apr 8, 2021Updated 5 years ago
- ☆10Jul 24, 2022Updated 4 years ago
- Useful Collective Variables for OpenMM☆23Oct 21, 2026Updated last week
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Oct 21, 2020Updated 6 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.
- Using supervised machine learning to build collective variables for accelerated sampling☆28Jun 26, 2018Updated 8 years ago
- ☆24Jan 16, 2024Updated 2 years ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆31Dec 19, 2021Updated 4 years ago
- Unified Free Energy Dynamics (UFED) simulations with OpenMM☆38Oct 17, 2026Updated 2 weeks ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆77Jun 12, 2023Updated 3 years ago
- Jupyter Notebook showing how to plot FES, histograms and time-series data using Matplotlib.☆13Dec 21, 2020Updated 5 years ago
- BioMetAll is a command line application to allow the identification of metal-binding sites in proteins from backbone preorganization.☆13Jun 9, 2026Updated 4 months ago
- Rigid Body Dynamics with OpenMM☆13May 29, 2018Updated 8 years ago
- Tools to build coarse grained models and perform simulations with OpenMM☆24Aug 12, 2026Updated 2 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Python code for generating Boresch restraints from MD simulations☆23Oct 11, 2025Updated last year
- Finding a lowest-energy pathway on a multidimensional landscape☆10Aug 4, 2023Updated 3 years ago
- Package for reading, analysis and visualization of metadynamics HILLS with 3 collective variables (addendum to metadynminer)☆11Apr 29, 2022Updated 4 years ago
- Rethinking Metadynamics: From Bias Potentials to Probability Distributions☆16Sep 18, 2023Updated 3 years ago
- Skipping the replica exchange ladder with normalizing flows☆13Feb 7, 2024Updated 2 years ago
- Gaussian accelerated Molecular Dynamics in OpenMM☆10Jan 7, 2025Updated last year
- Accelerating Metadynamics-Based Free-Energy Calculations with Adaptive Machine Learning Potentials☆18Jun 9, 2021Updated 5 years ago
- ☆11Oct 18, 2019Updated 7 years ago
- ☆19Aug 18, 2026Updated 2 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Tools for preparation and analysis of systems for molecular dynamics.☆32Dec 5, 2025Updated 10 months ago
- ML-based molecular representation models using PyTorch☆16Sep 17, 2026Updated last month
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Apr 16, 2026Updated 6 months ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆20Updated this week
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆44Apr 27, 2026Updated 6 months ago
- Houses deployable code for the SCORCH scoring function and docking pipeline from the related publication: https://doi.org/10.1016/j.jare.…☆18Nov 29, 2022Updated 3 years ago
- Cryptic pocket prediction using AlphaFold 2☆25Nov 27, 2022Updated 3 years ago
- ☆12Jul 31, 2020Updated 6 years ago
- Predicting water moelcule placements on protein surfaces using flow matching conditioned on learned protein structure embeddings.☆17Sep 17, 2026Updated last month
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆18Nov 2, 2024Updated 2 years ago
- SOURSOP is an analysis suite for molecular simulations of intrinsically disordered proteins☆12Oct 1, 2026Updated last month
- Genetic algorithm to convert 3D-RISM solvent densities to explicit water molecules in binding pockets☆13Dec 19, 2017Updated 8 years ago
- ☆13Sep 29, 2023Updated 3 years ago
- Enhanced protein mutational sampling using time-lagged variational autoencoders☆30Sep 17, 2018Updated 8 years ago
- McDock: Simple Monte Carlo docking algorithm in C++☆11Feb 10, 2017Updated 9 years ago
- NAMD QM/MM Tutorial on Free Energy Profile of Reaction Mechanisms☆17Sep 14, 2018Updated 8 years ago