Adding Additional Functionality and Enhancements to the Fetcher Module
Contributor: jauy123
A major goal for MDAnalysis 3.0 is the “support for streaming and cloud stor- age.”1. A natural extension of this object simply adding the ability to...
Science and medicine
MDAnalysis
Analysis of molecular simulations data with Python
Technologies
CC++cythonPython
Topics
computational-chemistryhigh-performance-computingmachine learningmolecular-simulationscience
- Total projects
- 19
- Years participating
- 7
- Most recent
- 2026
Participation history
Historical projects
Interface for post-simulation analysis (“crawling”) of WESTPA simulations
Contributor: Kunj Sinha
This project aims to implement a WESTPAParser and a WESTPAReader in WESTPA which will expose WESTPA’s HDF5 Framework simulation data as a standard...
Dashboard for tracking MD simulation progress with the new streaming interface
Contributor: Pardhav Maradani
This project will develop a browser-based, real-time dashboard for molecular dynamics simulations using the new IMDv3 streaming protocol, enabling...
Integrating MDAnalysis streaming analysis within WESTPA propagators
Contributor: Jamie Rowe
Weighted ensemble (WE) simulations enhance the exploration of a molecular system’s phase space by running numerous short, parallel simulations and...
Enhancing ProLIF Visualizations: A Hybrid Approach for Automated, Customizable 2D Interaction Layout
Contributor: Nilay Verma
ProLIF’s current 2D interaction diagrams often suffer from overlapping protein residues and tangled edges due to reliance on a default physics engine...
Better interfacing of Blender and MDAnalysis
Contributor: Pardhav Maradani
Blender is an industry leading open-source 3D modelling and animation software. MDAnalysis is an open-source Python library for analyzing molecuar...
MDAnalysis x ProLIF Project 5: H-Bond interactions from implicit hydrogens
Contributor: Yu-Yuan (Stuart) Yang
ProLIF, a tool for identifying protein-molecule interactions in molecular dynamics trajectories, lacks a straightforward method for evaluating...
2D visualization for small molecules
Contributor: Valerij Talagayev
The proposed project will revolve around the 2D visualization of chemical molecules. Currently MDAnalysis has a tool, which allows the conversion of...
Zarrtraj: Streaming H5MD trajectories from cloud services into MDAnalysis using Zarr
Contributor: Lawson
Adding support for streaming and cloud storage is one of the major themes of improvement for MDAnalysis 3.0. Achieving this goal will improve the...
Extend MDAnalysis Interoperability with OpenBabel
Contributor: Luna Morrow
Direct interoperability between molecular dynamics software is critical for enabling collaboration, data transfer and easy use by scientists....
Project 5: Implementation of parallel analysis in MDAnalysis
Contributor: Egor Marin
The proposal introduces parallel backend based on `dask` for MDAnalysis package. Potentially, it will allow researchers to run analysis of the...
Add Calculations for Self-Diffusivity and Viscosity
Contributor: Xu Hong Chen
MDAnalysis provides minimal support for calculating transport properties, measurable values which define the transfer of mass, heat, momentum, or...
Adding Energy Readers to MDAnalysis
Contributor: BFedder
In molecular dynamics simulations, users frequently have to inspect energy-like terms such as potential or kinetic energy, temperature, or pressure....
Context-aware guesser (implementing PDB and Martini guessers)
Contributor: Aya M. Alaa
MDAnalysis deals with various topologies with different structures, each of which has its specifications for presenting its data. The challenge is...
MDAnalysis module to calculate membrane curvature
Contributor: Estefania Barreto-Ojeda
Elements of differential geometry enable us to quantify the curvature of a surface. The core elements of biological membranes, phospholipids, provide...
A Solvation Module for MDAnalysis
Contributor: orion cohen
MDanalysis (MDA) is a powerful open-source package for exploring and performing calculations on molecular dynamics trajectories. Despite MDAs broad...
From RDKit to the Universe and back
Contributor: Cédric Bouysset
The aim of the RDKit interoperability project is to give MDAnalysis the ability to use RDKit’s Chem.Mol structure as an input to an MDAnalysis’...
Serialize Universes for parallel
Contributor: Yuxuan Zhuang
MDAnalysis is a flexible and relatively fast framework for complex analysis tasks in molecular dynamics (MD) simulations. To achieve a flawless...
Trajectory New Generation: the trajectory format for the future of simulation
Contributor: Hugo MacDermott-Opeskin
Trajectory storage has always proved problematic for the molecular simulation community, as large volumes of data can be generated quickly....