A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD
☆16Apr 3, 2026Updated 4 months ago
Alternatives and similar repositories for SAFEP_tutorial
Users that are interested in SAFEP_tutorial are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- This repository contained python code used to do organic free energy calculation. Reference: http://www.bevanlab.biochem.vt.edu/Pages/Per…☆11Aug 2, 2018Updated 8 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆76Jun 30, 2026Updated last month
- Tautomer ratios in solution☆28Sep 20, 2021Updated 4 years ago
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆20Aug 14, 2020Updated 5 years ago
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated last year
- 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.
- ☆11Oct 18, 2019Updated 6 years ago
- This script is designed for evaluating the binding affinity between a protein target and a small molecule, by calculating the binding fre…☆15May 1, 2023Updated 3 years ago
- ☆13Dec 29, 2022Updated 3 years ago
- ☆10May 17, 2021Updated 5 years ago
- ☆23Aug 25, 2023Updated 2 years ago
- Bias-controlled 3D generative framework for structure-based ligand design☆17Nov 2, 2022Updated 3 years ago
- EnzyDock: Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes☆18Sep 5, 2024Updated last year
- Python optimisation of atomistic ligand charges to maximize receptor binding affinity☆12Aug 3, 2020Updated 6 years ago
- ☆90Jul 19, 2023Updated 3 years ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆211Sep 22, 2023Updated 2 years ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆172Aug 2, 2026Updated last week
- Some practical theoretic background needed for running MD simulations☆23Jun 2, 2026Updated 2 months ago
- ☆37Jun 10, 2025Updated last year
- Software package for FEP☆23Updated this week
- ☆14Jul 11, 2026Updated 3 weeks ago
- Examples for use of YANK - getyank.org☆12Sep 20, 2021Updated 4 years ago
- MMTSB Tool Set☆33Jan 26, 2026Updated 6 months ago
- Set up relative free energy calculations using a common scaffold☆24Apr 21, 2026Updated 3 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.
- Enhanced sampling methods for molecular dynamics simulations☆46Dec 16, 2022Updated 3 years ago
- PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Comp…☆17Mar 18, 2026Updated 4 months ago
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆29Updated this week
- 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
- binding free energy estimator 2☆146Jul 29, 2026Updated last week
- TUPÃ: Electric field analyses for molecular simulations☆25Jun 12, 2026Updated last month
- ☆21May 28, 2025Updated last year
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆140May 24, 2024Updated 2 years ago
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆34Jun 3, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- ☆23Oct 2, 2024Updated last year
- Fast PBC wrapping and unwrapping for VMD☆27Nov 25, 2024Updated last year
- A semi-automated force field converter for GROMACS. Enables users to easily convert a system between two all-atom force fields. Requires …☆17Aug 1, 2026Updated last week
- User Guide for MDAnalysis☆30Updated this week
- Bayesian Multistate Bennett Acceptance Ratio Method☆16Jun 28, 2026Updated last month
- ☆19Jul 8, 2022Updated 4 years ago
- Dynamics PyMOL Plugin☆49Apr 19, 2024Updated 2 years ago