Parallel algorithms for MDAnalysis
☆31Aug 2, 2024Updated last year
Alternatives and similar repositories for pmda
Users that are interested in pmda are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Reads Gromacs EDR file to populate a pandas dataframe☆34Oct 12, 2025Updated 9 months ago
- Molecular kaleidoscope☆15Apr 11, 2018Updated 8 years ago
- Python bindings for TNG file format☆13Oct 14, 2025Updated 9 months ago
- MDAnalysis wrapper around Packmol☆37May 1, 2023Updated 3 years ago
- a quick primer on making prettier (and more impactful) plots☆14Sep 27, 2015Updated 10 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.
- Access to data for workshops and extended tests of MDAnalysis.☆19Apr 3, 2026Updated 3 months ago
- Command line interface for MDAnalysis☆23Jul 1, 2026Updated 2 weeks ago
- User Guide for MDAnalysis☆30Updated this week
- Best Practices article intended for LiveCoMS☆43Mar 26, 2026Updated 3 months ago
- persistent, pythonic trees for heterogeneous data☆33May 20, 2022Updated 4 years ago
- MDAnalysis home page mdanalysis.org as GitHub pages.☆14Updated this week
- Analysis of Molecular Dynamics output in the IPython Notebook☆10Jan 24, 2017Updated 9 years ago
- Optimization tool for calibrating coarse-grained force fields of lipids, relying on the simultaneous usage of reference AA trajectories (…☆10Jun 6, 2023Updated 3 years ago
- Implementation of MOFF force field. Please cite us at Latham, A; Zhang, B J. Chem. Theory Comput. 2021, 17, 3134. (https://pubs.acs.org/d…☆11Jun 16, 2022Updated 4 years ago
- 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.
- Analysis of non-covalent interactions in MD trajectories☆69Jan 3, 2025Updated last year
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆29May 2, 2020Updated 6 years ago
- Quickly generate, start and analyze benchmarks for molecular dynamics simulations.☆84Sep 5, 2024Updated last year
- Force Distribution Analysis (FDA) for GROMACS☆36Jun 18, 2024Updated 2 years ago
- A comprehensive tool for analyzing liquid solvation structure.☆54Nov 26, 2025Updated 7 months ago
- MDAnalysis Tutorial at the 2015 CECAM Macromolecular simulation software workshop☆13Jul 22, 2016Updated 9 years ago
- An extension to the MDAnalysis library providing support for dealing with structural ensembles. There is currently support for calculatin…☆16Jul 20, 2018Updated 8 years ago
- a logistics and persistence engine for the analysis of molecular dynamics trajectories☆30Jan 24, 2020Updated 6 years ago
- The integrated tempering sampling as a bias in PLUMED2☆11Jan 15, 2021Updated 5 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Calculation of water/solvent partition coefficients with Gromacs.☆29Oct 14, 2024Updated last year
- Simple library for reading trajectory coordinates☆18Oct 5, 2016Updated 9 years ago
- Flexible storage of chemical topology for molecular simulation☆71Updated this week
- ☆11Oct 18, 2019Updated 6 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 7 years ago
- A tool to characterize the local structure of liquid water by geometric order parameters.☆15Jul 31, 2024Updated last year
- Advanced toolkit for binding free energy calculations☆36Sep 2, 2025Updated 10 months ago
- CHAP is a tool for the functional annotation of ion channel structures:☆22Jan 17, 2024Updated 2 years ago
- Repository of the data for PLUMED Masterclass 22.3☆15Jul 10, 2024Updated 2 years ago
- 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.
- Installable VMD as a python module☆154Jun 10, 2025Updated last year
- Automatic MARTINI parametrization of small organic molecules☆76May 28, 2025Updated last year
- The MDAnalysis Toolkits Registry☆19Updated this week
- Python module for parsing, writing, aligning, and manipulating glycan structrures☆10Jun 23, 2026Updated 3 weeks ago
- A package for deriving coarse-grain potentials using MultiState Iterative Boltzmann Inversion (MS-IBI)☆20Jun 2, 2026Updated last month
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆20Updated this week
- Statistical models for biomolecular dynamics☆44May 8, 2025Updated last year