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Science and medicine

MDAnalysis

Analysis of molecular simulations data with Python

cc++cythonpython
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Participation history

7 GSoC years

2026202520242023202220212020

2026

3 projects

Official year page

Adding Additional Functionality and Enhancements to the Fetcher Module

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...

Project page

Interface for post-simulation analysis (“crawling”) of WESTPA simulations

This project aims to implement a WESTPAParser and a WESTPAReader in WESTPA which will expose WESTPA’s HDF5 Framework simulation data as a standard...

Project page

Dashboard for tracking MD simulation progress with the new streaming interface

This project will develop a browser-based, real-time dashboard for molecular dynamics simulations using the new IMDv3 streaming protocol, enabling...

Project page

2025

4 projects

Official year page

Integrating MDAnalysis streaming analysis within WESTPA propagators

Weighted ensemble (WE) simulations enhance the exploration of a molecular system’s phase space by running numerous short, parallel simulations and...

CodeProject page

Enhancing ProLIF Visualizations: A Hybrid Approach for Automated, Customizable 2D Interaction Layout

ProLIF’s current 2D interaction diagrams often suffer from overlapping protein residues and tangled edges due to reliance on a default physics engine...

CodeProject page

Better interfacing of Blender and MDAnalysis

Blender is an industry leading open-source 3D modelling and animation software. MDAnalysis is an open-source Python library for analyzing molecuar...

CodeProject page

MDAnalysis x ProLIF Project 5: H-Bond interactions from implicit hydrogens

ProLIF, a tool for identifying protein-molecule interactions in molecular dynamics trajectories, lacks a straightforward method for evaluating...

CodeProject page

2024

3 projects

Official year page

2D visualization for small molecules

The proposed project will revolve around the 2D visualization of chemical molecules. Currently MDAnalysis has a tool, which allows the conversion of...

CodeProject page

Zarrtraj: Streaming H5MD trajectories from cloud services into MDAnalysis using Zarr

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...

CodeProject page

Extend MDAnalysis Interoperability with OpenBabel

Direct interoperability between molecular dynamics software is critical for enabling collaboration, data transfer and easy use by scientists....

CodeProject page

2023

2 projects

Official year page

Project 5: Implementation of parallel analysis in MDAnalysis

The proposal introduces parallel backend based on `dask` for MDAnalysis package. Potentially, it will allow researchers to run analysis of the...

CodeProject page

Add Calculations for Self-Diffusivity and Viscosity

MDAnalysis provides minimal support for calculating transport properties, measurable values which define the transfer of mass, heat, momentum, or...

CodeProject page

2022

2 projects

Official year page

Adding Energy Readers to MDAnalysis

In molecular dynamics simulations, users frequently have to inspect energy-like terms such as potential or kinetic energy, temperature, or pressure....

CodeProject page

Context-aware guesser (implementing PDB and Martini guessers)

MDAnalysis deals with various topologies with different structures, each of which has its specifications for presenting its data. The challenge is...

CodeProject page

2021

2 projects

Official year page

MDAnalysis module to calculate membrane curvature

Elements of differential geometry enable us to quantify the curvature of a surface. The core elements of biological membranes, phospholipids, provide...

CodeProject page

A Solvation Module for MDAnalysis

MDanalysis (MDA) is a powerful open-source package for exploring and performing calculations on molecular dynamics trajectories. Despite MDAs broad...

CodeProject page

2020

3 projects

Official year page

From RDKit to the Universe and back

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’...

CodeProject page

Serialize Universes for parallel

MDAnalysis is a flexible and relatively fast framework for complex analysis tasks in molecular dynamics (MD) simulations. To achieve a flawless...

CodeProject page

Trajectory New Generation: the trajectory format for the future of simulation

Trajectory storage has always proved problematic for the molecular simulation community, as large volumes of data can be generated quickly....

CodeProject page