Tutorials on doing AMBER based Metadynamics and Gaussian Accelerated MD (GaMD)
☆11Dec 1, 2025Updated 3 months ago
Alternatives and similar repositories for Enhanced-Sampling-in-AMBER-tutorial
Users that are interested in Enhanced-Sampling-in-AMBER-tutorial are comparing it to the libraries listed below
Sorting:
- Temperature generator for Replica Exchange MD simulations☆29Dec 14, 2022Updated 3 years ago
- A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations☆13Feb 20, 2023Updated 3 years ago
- Fragment Linker Prediction Using Deep Encoder-Decoder Network for PROTAC Drug Design☆12Oct 2, 2023Updated 2 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 6 years ago
- Tutorials and additional documentation for the WESTPA suite☆16Oct 20, 2025Updated 4 months ago
- A tutorials suite for BioSimSpace.☆34Oct 22, 2025Updated 4 months ago
- Accelerating Metadynamics-Based Free-Energy Calculations with Adaptive Machine Learning Potentials☆17Jun 9, 2021Updated 4 years ago
- ☆16Dec 24, 2016Updated 9 years ago
- Tutorial to build AMBER compatable protein+lipid systems☆16Apr 19, 2017Updated 8 years ago
- UROP Project @ Coley Group☆27Jan 22, 2023Updated 3 years ago
- Integrative modeling of PROTAC-mediated ternary complex☆29May 4, 2022Updated 3 years ago
- Software tools for fragment-based drug discovery (FBDD)☆27Apr 6, 2020Updated 5 years ago
- Example files for Colvars module: https://github.com/Colvars/colvars☆13Dec 7, 2021Updated 4 years ago
- ☆31Jan 26, 2026Updated last month
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆74Aug 11, 2023Updated 2 years ago
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆29Jun 3, 2024Updated last year
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆48Feb 11, 2021Updated 5 years ago
- Molecular visualization for MDAnalysis with MolecularNodes in Blender☆18Mar 30, 2025Updated 11 months ago
- SST2 implementation in openmm☆19Jan 19, 2026Updated last month
- Generate Ramachandran plots for single PDB structure and as heatmap for MD trajectory☆11Apr 6, 2022Updated 3 years ago
- Rapid construction of chemical pipelines in interactive notebooks and cli usage☆13Sep 27, 2024Updated last year
- ☆32Sep 23, 2023Updated 2 years ago
- Pras Server is a library to repair PDB or mmCIF structures, add missing heavy atoms and hydrogen atoms and assign secondary structure by …☆28Aug 10, 2025Updated 6 months ago
- Learning free energy landscapes using artificial neural networks☆14Nov 30, 2017Updated 8 years ago
- Molecular conformer generation using enhanced sampling methods☆20Jul 28, 2025Updated 7 months ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆31Dec 19, 2021Updated 4 years ago
- ☆25Jan 16, 2024Updated 2 years ago
- PyEMMA Jupyter Notebooks☆14Jan 28, 2021Updated 5 years ago
- ☆18Jul 29, 2025Updated 7 months ago
- A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling metho…☆22Sep 26, 2024Updated last year
- Automatic CHARMM-GUI browser interaction with Python☆18Mar 20, 2023Updated 2 years ago
- Repository of the data for PLUMED Masterclass 22.3☆14Jul 10, 2024Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Dec 10, 2023Updated 2 years ago
- Highly parallel molecular docking pipeline using Vina-GPU (dockerized) + AutoDock Vina CPU☆17Nov 19, 2024Updated last year
- Package for reading, analysis and visualization of metadynamics HILLS☆39Nov 28, 2023Updated 2 years ago
- Alchemical mutation scoring map☆41Nov 21, 2025Updated 3 months ago
- PiViewer: an open-source tool for automated detection and display of pi-pi interactions☆14Jun 6, 2018Updated 7 years ago
- Useful Collective Variables for OpenMM☆17May 9, 2024Updated last year
- Material for the 3rd i-CoMSE Workshop: Methods for Advanced Sampling☆42May 1, 2023Updated 2 years ago