Examples of applications of pymbar to various problems in simulation and experiment
☆24Jan 16, 2015Updated 11 years ago
Alternatives and similar repositories for pymbar-examples
Users that are interested in pymbar-examples are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆45Jan 29, 2026Updated 9 months ago
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆28Oct 21, 2026Updated last week
- ☆32Jul 8, 2026Updated 3 months ago
- Analysis of non-covalent interactions in MD trajectories☆72Jan 3, 2025Updated last year
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 7 years 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.
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆140May 24, 2024Updated 2 years ago
- Software for automated processing of alchemical free energy calculations☆12Nov 7, 2022Updated 3 years ago
- Workshop on the preparation, execution, and analysis of protein molecular dynamics simulations☆12May 7, 2025Updated last year
- Python implementation of the multistate Bennett acceptance ratio (MBAR)☆319Feb 12, 2026Updated 8 months ago
- Jupyter Notebook showing how to plot FES, histograms and time-series data using Matplotlib.☆13Dec 21, 2020Updated 5 years ago
- Workshops on Computational Biology organized by our lab☆10Mar 25, 2024Updated 2 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Dec 10, 2023Updated 2 years ago
- 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
- A free energy command line tool using alchemlyb☆17Dec 11, 2022Updated 3 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Sample code from Allen & Tildesley's Computer Simulation of Liquids, 1st Ed. See https://github.com/Allen-Tildesley/examples for moderni…☆18Sep 10, 2017Updated 9 years ago
- ☆10Jul 11, 2021Updated 5 years ago
- Some of useful tcl scripts to analyse data from VMD☆16Aug 2, 2022Updated 4 years ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Oct 27, 2022Updated 4 years ago
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆19Apr 16, 2025Updated last year
- Molecular simulation toolkit☆20Sep 6, 2026Updated last month
- References, presentations and other resources☆15Oct 31, 2023Updated 3 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Feb 11, 2021Updated 5 years ago
- Probabilistic Inference for NOvel Therapeutics☆15Feb 5, 2022Updated 4 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- The Surface Assessment via Grid Evaluation (SuAVE) software was developed to account for the effect of curvature in the calculations of s…☆12Jun 7, 2026Updated 4 months ago
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆22May 14, 2025Updated last year
- A tool to create molecule structures from topology information (GROMACS-only)☆11Feb 23, 2026Updated 8 months ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆20Updated this week
- ☆32Feb 24, 2022Updated 4 years ago
- A Python/Fortran order parameter analysis library☆14Dec 22, 2020Updated 5 years ago
- Data and model repository for the ASKCOS application☆16Feb 24, 2022Updated 4 years ago
- Robust and stable clustering of molecular dynamics simulation trajectories.☆20Sep 2, 2022Updated 4 years ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆174Aug 18, 2026Updated 2 months ago
- 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.
- Best practice document for alchemical free energy calculations going to livecoms journal☆94May 28, 2026Updated 5 months ago
- OpenMM plugin for simulating electrochemical systems☆22Sep 23, 2024Updated 2 years ago
- Finding a lowest-energy pathway on a multidimensional landscape☆10Aug 4, 2023Updated 3 years ago
- Advanced toolkit for binding free energy calculations☆36Sep 2, 2025Updated last year
- Scripts for PCA and related analyses of lipid motions☆10Jun 21, 2022Updated 4 years ago
- Python optimisation of atomistic ligand charges to maximize receptor binding affinity☆12Aug 3, 2020Updated 6 years ago
- ☆26Jun 16, 2025Updated last year