MDAnalysis is a library for the analysis of computational (primarily
molecular dynamics, i.e. MD) simulations. Frequently these analyses
are rare, novel, or individual enough that they are not immediately
available as a predefined function within MDAnalysis. MDAnalysis
provides a toolkit for interacting with simulations and constructing
new analyses. Lily will create a high-level user guide structured by
topic. This user guide will describe the building blocks of the data
structures, analysis, topologies, and more. It will be targeted at a
general audience; molecular dynamics users will be able to see the
machine abstraction and technical considerations (e.g. MemoryReader)
under the hood, while developers will be able to gain an understanding
of the scientific background.
Lily Wang is a Ph.D. student at the Australian National University,
Canberra. She aims to improve various aspects of molecular dynamics
simulation over the course of her degree. During GSoD, she hopes to
refine her technical writing skills while contributing to a package
that she very much appreciates. In the tattered remnants of her free
time, she enjoys reading and wandering around mountains. You can
follow her progress on GSoD (and reading) on her
blog.
We are happy to anounce that MDAnalysis is hosting one GSoC
students for NumFOCUS this year, Ninad Bhat (@NinadBhat) on GitHub).
Ninad Bhat: Better Periodic Boundary Handling
Molecular simulations are predominantly ran under periodic boundary
conditions, i.e., upon leaving one face of the simulation volume, you
re-enter in the opposite face. This can lead to molecules being split
over the periodic boundary, which requires rectification before
performing calculations. In this project, Ninad will implement
wrapping and unwrapping functionality in the various AtomGroup methods
that use the position of particles, e.g., the calculation of the
center of mass. In order to improve performance, the wrapping and
unwrapping methods will be implemented in Cython.
Ninad is a senior undergraduate at IIT Bombay. He is working with
Phase Field Modelling for his master thesis and has also used
molecular dynamics for some of his projects. He has been contributing
to different open source projects since 2016 and credits most of his
programming knowledge to it. During GSoC, he aims to improve his
software development skills while also getting a deeper understanding
of molecular dynamics.
MDAnalysis was accepted for Google Season of Docs 2019. We
are proud to be one of 50 participating open source
organizations, which span all reaches of open
source and includes the Wikimedia Foundation, NumPy and SciPy, the
CERN High Energy Software Foundation, Drupal, Arduino, LLVM Compiler
Infrastructure, and many more outstanding projects that really have
been moving the open source community forward.
We would love to have a technical writer work with us to improve our
documentation. If you want to work with scientists that write code to
do science at the molecular scale then please contact us on the
developer list.
Apply now.
The deadline for applications is June 28, 2019 at 18:00 UTC.
More about Projects and MDAnalysis
Our recent post on our GSoD application
explains more of the background and summarizes our project ideas.
MDAnalysis is a project written by scientists for scientists and is
currently used for cutting edge research around the world.
A writer with MDAnalysis will learn about the
technical aspects of creating docs for open source code (such as
documentation generation with Sphinx, continuous integration-based
workflows and distributed development with git via our GitHub
source code repository) and also about the science that MDAnalysis
enables. Our developers have published many scientific publications
that used our library or described innovative new methods that were
implemented in MDAnalysis. A writer will interact with these
accomplished scientists and learn about the science: How
molecules are simulated (e.g., biomolecules such as proteins and DNA or
novel materials) and how scientists analyze such simulations in order
to better understand the world at the microscopic scale.
The video shows the result of a molecular dynamics simulation in which
a sodium ion (magenta sphere) together with water molecules
(red/white “L” shapes) bind to a protein (shown in
cartoon representation as blue and green
ribbons), a process that is important in maintaining the health of
cells in the body. The MDAnalysis package enables us to write code
which can perform calculations on these results,
here allowing us to quantify the interaction
between the ion and the protein and generate fundamental understanding
of important processes in living beings.
Contact
If you have any questions or if you want to work with us please write to us on the
developer list.
