Tutorials for non-Markovian dynamic models (qMSM and IGME) to study protein dynamics.
☆27Aug 15, 2024Updated 2 years ago
Alternatives and similar repositories for GME_tutorials
Users that are interested in GME_tutorials are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Combines FRESEAN mode analysis of a protein (based on a CG representation) with enhanced sampling using metadynamics☆17May 7, 2026Updated 5 months ago
- A step-by-step tutorial to run Molecular Dynamics Simulations with enhanced sampling of a pepitide using PLUMED implemented in GROMACS to…☆16Mar 4, 2024Updated 2 years ago
- Subset of AmberTools, with updates and modifications☆25Sep 29, 2026Updated last week
- [ICML 2025] Repurposing pre-trained score-based generative models for transition path sampling by minimizing the Onsager-Machlup (OM) act…☆30Mar 20, 2026Updated 6 months ago
- A conda-smithy repository for ambertools.☆13Jul 15, 2026Updated 2 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- TS-DAR identifies transition states of protein conformational changes from MD simulations using hyperspherical embeddings in the latent s…☆21May 15, 2026Updated 4 months ago
- A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling metho…☆25Sep 26, 2024Updated 2 years ago
- Tutorials and additional documentation for the WESTPA suite☆16Sep 30, 2026Updated last week
- ☆15Jun 11, 2024Updated 2 years ago
- Repository of the data for PLUMED Masterclass 22.3☆15Jul 10, 2024Updated 2 years ago
- Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE)☆44May 3, 2020Updated 6 years ago
- Coarse-grained simulations of biomolecular complexes☆13Aug 2, 2023Updated 3 years ago
- Quantum to Molecular Mechanics (Q2MM)☆25Sep 4, 2026Updated last month
- Helper function for Markov State Models☆11Jun 25, 2024Updated 2 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆19Jun 6, 2023Updated 3 years ago
- Generative backmapping of coarse-grained molecular systems using an equivariant graph neural network and flow-matching☆12Sep 17, 2025Updated last year
- mdml: Deep Learning for Molecular Simulations☆55May 17, 2025Updated last year
- Statistical models for biomolecular dynamics☆44May 8, 2025Updated last year
- Correlation-based feature selection of Molecular Dynamics simulations☆29Aug 18, 2026Updated last month
- Software package for FEP☆24Aug 7, 2026Updated 2 months ago
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆64Aug 5, 2026Updated 2 months ago
- A tutorials suite for BioSimSpace.☆37Oct 22, 2025Updated 11 months ago
- Computational Statistical Mechanics Tutorials☆15Nov 29, 2012Updated 13 years 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.
- Comparison of principal components analysis with diffusion maps on toy data sets and a molecular simulation trajectory☆17Feb 1, 2017Updated 9 years ago
- ☆17Oct 30, 2023Updated 2 years ago
- Program for robust fitting of bonded Molecular Mechanics parameters☆15Jun 30, 2015Updated 11 years ago
- Software for automated processing of alchemical free energy calculations☆12Nov 7, 2022Updated 3 years ago
- MDverse web scrapper 🔎🔧📄☆15Feb 21, 2026Updated 7 months ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆76Jun 30, 2026Updated 3 months ago
- Python implementation of the multistate Bennett acceptance ratio (MBAR)☆318Feb 12, 2026Updated 8 months ago
- Deep generative modeling of protein structural ensembles☆41May 27, 2026Updated 4 months ago
- This repository provides with custom code and analysis scripts to generate structural ensembles of intrinsically disordered proteins by u…☆24Oct 31, 2025Updated 11 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Demo of diffusion models #DDPM applied to molecular dynamics of small peptide☆14Jan 26, 2024Updated 2 years ago
- ASGARD is a tool that allows via an automated MD workflow to perform MD protein or protein-ligand complex analysis and to generate the co…☆19Jul 11, 2024Updated 2 years ago
- ☆11May 12, 2026Updated 5 months ago
- Gibbs sampling for expanded ensembles and replica exchange simulations☆11Jun 1, 2014Updated 12 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆29Dec 4, 2024Updated last year
- A fast sampling and analysis tool for biomolecules☆18Aug 2, 2026Updated 2 months ago
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆16Jul 2, 2024Updated 2 years ago