This repository contained python code used to do organic free energy calculation. Reference: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html; https://github.com/ruanyangry/gromacs-lammps-process-simulation.
☆11Aug 2, 2018Updated 7 years ago
Alternatives and similar repositories for gromacs-free-energy-calculation
Users that are interested in gromacs-free-energy-calculation are comparing it to the libraries listed below
Sorting:
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆15Mar 2, 2026Updated last week
- A collection of scripts which I have developed to use GROMACS, for both compute clusters and post-simulation analysis.☆11Jul 15, 2014Updated 11 years ago
- ParametrizANI - Fast, Accurate and Free Dihedral Parametrization in the Cloud with TorchANI☆22Jul 28, 2025Updated 7 months ago
- Tutorials of codes such as VASP, Quantum Espresso and Lammps☆14Sep 13, 2025Updated 5 months ago
- This reaxFF LAMMPS script can be used to simulate the oxidation of nanomaterials, followed by cooling and thermal equilibration. Finally,…☆13Jul 29, 2022Updated 3 years ago
- Postprocessing of Lammps outfile to analyze ReaxFF dyanamics data☆13Apr 27, 2019Updated 6 years ago
- ☆14Jul 7, 2016Updated 9 years ago
- Screening protocol with AUTODOCK-GPU☆14Feb 27, 2023Updated 3 years ago
- ☆14Jul 16, 2020Updated 5 years ago
- Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Groma…☆38Aug 2, 2018Updated 7 years ago
- ☆22Aug 25, 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
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆19Aug 14, 2020Updated 5 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 3 years ago
- Solvation Structure and Thermodynamic Mapping☆42Dec 17, 2025Updated 2 months ago
- The OpenMM Cookbook and Tutorials☆56Feb 11, 2026Updated 3 weeks ago
- Package to perform minimum-distance distribution analyses of complex solute-solvent interactions☆23Feb 25, 2026Updated last week
- Python code for generating Boresch restraints from MD simulations☆22Oct 11, 2025Updated 4 months ago
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆24Jun 8, 2024Updated last year
- Some practical theoretic background needed for running MD simulations☆21Aug 1, 2025Updated 7 months ago
- OnionNet-2 is constructed based on convolutional neural network (CNN) to predict the protein-ligand binding affinity.☆24Mar 2, 2024Updated 2 years ago
- TUPÃ: Electric field analyses for molecular simulations☆23Feb 14, 2026Updated 3 weeks ago
- ☆28Jan 9, 2024Updated 2 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆28Dec 4, 2024Updated last year
- Set up relative free energy calculations using a common scaffold☆24Aug 19, 2025Updated 6 months ago
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆34Jan 6, 2026Updated 2 months ago
- Open Source Antibiotics Series 2☆10Jan 23, 2023Updated 3 years ago
- Tautomer ratios in solution☆28Sep 20, 2021Updated 4 years ago
- A library to align rigid molecules and clusters☆12Updated this week
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆29Nov 2, 2025Updated 4 months ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆30Jan 23, 2024Updated 2 years ago
- ☆70Jul 19, 2023Updated 2 years ago
- Materials for the 2021 PRACE Workshop @ SurfSARA☆30Nov 11, 2021Updated 4 years ago
- Python tutorial for estimating and clustering free energy landscapes with InfleCS.☆31May 6, 2022Updated 3 years ago
- Learning Binding Affinities via Fine-tuning of Protein and Ligand Language Models☆37Dec 5, 2024Updated last year
- This package contains tools for setting up hybrid-topology FE calculations☆38Mar 2, 2026Updated last week
- Simulation Input/Output for LAMMPS with ReaxFF for Atomistic Corrosion Modelling☆33May 14, 2019Updated 6 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆74Jan 30, 2026Updated last month
- Force Distribution Analysis (FDA) for GROMACS☆35Jun 18, 2024Updated last year