Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.
☆15Sep 20, 2018Updated 7 years ago
Alternatives and similar repositories for hop
Users that are interested in hop are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- MDAnalysis Tutorial at the 2015 CECAM Macromolecular simulation software workshop☆13Jul 22, 2016Updated 9 years ago
- pyMBE provides tools to facilitate building up molecules with complex architectures in the Molecular Dynamics software ESPResSo. For an…☆13Updated this week
- Python library to run structure based model (SBM) simulations using the OpenMM toolkit☆23Jan 16, 2026Updated 3 months ago
- a quick primer on making prettier (and more impactful) plots☆14Sep 27, 2015Updated 10 years ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆29May 2, 2020Updated 6 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.
- Playmol is a(nother) software for building molecular models☆19Mar 14, 2023Updated 3 years ago
- Gibbs sampling for expanded ensembles and replica exchange simulations☆11Jun 1, 2014Updated 11 years ago
- Examples and data for performing path similarity analysis (PSA).☆17Oct 23, 2015Updated 10 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 7 years ago
- Software for the prediction of DEER and PRE data from conformational ensembles.☆14May 6, 2025Updated last year
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆31Apr 4, 2026Updated last month
- This repo contains the codes to run solvation free energy prediction.☆12May 1, 2022Updated 4 years ago
- Predict allosteric pockets on proteins☆15Mar 28, 2022Updated 4 years ago
- Adaptive string method implementation in AmberTools23 and Amber22☆15Jan 7, 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.
- ☆14Jun 4, 2024Updated last year
- ☆16Jul 26, 2024Updated last year
- Atomistic Topology Operations in Matlab, scripts for manipulation of molecular dynamics or monte carlo simulation systems☆23Nov 27, 2025Updated 5 months ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆19Apr 23, 2026Updated last week
- Analyse Rotational Diffusion Tensor from MD Simulations☆22Oct 31, 2024Updated last year
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆34Jan 6, 2026Updated 3 months ago
- Calculation of water/solvent partition coefficients with Gromacs.☆29Oct 14, 2024Updated last year
- Hacking structural biology with Python and pandas☆21Nov 7, 2015Updated 10 years ago
- Useful Collective Variables for OpenMM☆18May 9, 2024Updated last year
- 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.
- calculate set voronoi diagrams☆10Oct 24, 2019Updated 6 years ago
- a Python program for running QM/MM simulations using Q-Chem and OpenMM☆16Apr 24, 2022Updated 4 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Apr 7, 2022Updated 4 years ago
- scripts for analyzing molecular dynamics trajectories using VMD☆40May 28, 2015Updated 10 years ago
- Constant pH simulation with OpenMM☆19Mar 10, 2026Updated last month
- Analysis of non-covalent interactions in MD trajectories☆69Jan 3, 2025Updated last year
- Automated tools for submitting molecules to QCFractal☆26Apr 24, 2026Updated last week
- // PROJECT PAUSED FOR NOW (lack of capacity) // Protein cavity identification and automatic subpocket decomposition☆46Jul 23, 2023Updated 2 years ago
- Correlation-based feature selection of Molecular Dynamics simulations☆29Mar 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.
- Different run and analysis scripts as described in the research guides.☆14Jul 5, 2022Updated 3 years ago
- python simulation interface for molecular modeling. To cite this software publication: https://www.sciencedirect.com/science/article/pii/…☆13Aug 24, 2016Updated 9 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆68Apr 16, 2021Updated 5 years ago
- Python script that creates 2D protein-ligand interaction images☆14Apr 23, 2018Updated 8 years ago
- A Matlab implementation for automatic segmentation with a graphical user interface☆17Apr 7, 2019Updated 7 years ago
- Conservation analysis of homologous proteins with Python☆13Jul 11, 2021Updated 4 years ago
- Using Gomacs from IPython notebook☆20Apr 8, 2014Updated 12 years ago