Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.
☆17Oct 20, 2026Updated last week
Alternatives and similar repositories for dcTMD
Users that are interested in dcTMD are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Correlation-based feature selection of Molecular Dynamics simulations☆29Aug 18, 2026Updated 2 months ago
- Helper function for Markov State Models☆11Jun 25, 2024Updated 2 years ago
- Robust and stable clustering of molecular dynamics simulation trajectories.☆20Sep 2, 2022Updated 4 years ago
- Selecting Features for Markov Modeling: A Case Study on HP35☆11May 25, 2023Updated 3 years ago
- ☆12May 20, 2019Updated 7 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Generalized Kraskov Estimator for Normalized Mutual Information☆23Updated this week
- A python implementation of the string method with swarms of trajectories using GROMACS☆21Oct 19, 2022Updated 4 years ago
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆29Jun 8, 2024Updated 2 years ago
- Set of tools to generate a multi-eGO force field to perform molecular dynamics simulations☆17Oct 23, 2026Updated last week
- Program Package for Sampling, Training and Applying ML-based Potential models☆13Oct 23, 2026Updated last week
- Combines FRESEAN mode analysis of a protein (based on a CG representation) with enhanced sampling using metadynamics☆17May 7, 2026Updated 5 months ago
- Cryptic pocket prediction using AlphaFold 2☆25Nov 27, 2022Updated 3 years ago
- ☆10Nov 22, 2022Updated 3 years ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Mar 7, 2025Updated last year
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- A python module to plot secondary structure schemes☆26Mar 18, 2026Updated 7 months ago
- ☆32Jul 8, 2026Updated 3 months ago
- A deep learning-based framework to uniquely identify an uncorrelated, isometric and meaningful latent representation.☆19Sep 12, 2023Updated 3 years ago
- Source code and input files associated to the paper "Targeted free energy perturbation revisited: Accurate free energies from mapped refe…☆13Sep 14, 2021Updated 5 years ago
- A python implementation of the Fast Stokesian Dynamics methods (A. Fiore, J. Swan, 2019) which leverage the library JAX to just-in-time c…☆11Dec 7, 2025Updated 10 months ago
- MDverse web scrapper 🔎🔧📄☆15Feb 21, 2026Updated 8 months 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
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Jan 26, 2022Updated 4 years ago
- Enhanced sampling in the representation space of atomistic neural networks.☆17Updated this week
- 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.
- Denoising diffusion probabilistic models for replica exchange☆23Feb 19, 2022Updated 4 years ago
- Computation of the drug-target relative residence times from RAMD simulations☆23Aug 29, 2024Updated 2 years ago
- Fast, parallelized implementation of Principal Component Analysis with constant memory consumption for large data sets.☆12Feb 18, 2022Updated 4 years ago
- Neural relational inference for molecular dynamics simulations☆60May 30, 2023Updated 3 years ago
- Demo of diffusion models #DDPM applied to molecular dynamics of small peptide☆14Jan 26, 2024Updated 2 years ago
- Generative backmapping of coarse-grained molecular systems using an equivariant graph neural network and flow-matching☆12Sep 17, 2025Updated last year
- The DPA package is the scikit-learn compatible implementation of the Density Peaks Advanced clustering algorithm. The algorithm provides…☆31Dec 30, 2021Updated 4 years ago
- Force Distribution Analysis (FDA) for GROMACS☆37Jun 18, 2024Updated 2 years ago
- OpenMM plugin to interface with PLUMED☆82Aug 31, 2026Updated last month
- 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.
- Jupyter Notebook showing how to plot FES, histograms and time-series data using Matplotlib.☆13Dec 21, 2020Updated 5 years ago
- A software research tool for the analysis of structural communication in protein ensembles☆15Mar 24, 2022Updated 4 years ago
- Entropy from PDB conformational ensembles☆13Mar 28, 2024Updated 2 years ago
- ☆14Feb 25, 2026Updated 8 months ago
- PyEMMA Jupyter Notebooks☆13Jan 28, 2021Updated 5 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆19Jun 6, 2023Updated 3 years ago
- Fast Stokesian Dynamics☆18Updated this week