GSOC 2021

[LEONARDO BARNESCHI]

Hello everyone, I am Leonardo Barneschi, a 2nd year PhD student in computational photochemistry and photobiology at the University of Siena, Italy. In my research I routinely use quantum chemistry and molecular dynamics programs, and Python to process data obtained from simulations, thus I am a regular MDAnalysis user. These analyses require extensive usage of Python libraries for scientific computing such as numpy, scipy or data analysis libraries such as Pandas.    

I would be interested in participating in the GSOC 2021 program with MDAnalysis developers to contribute to the package, to learn more about its structure and to improve my OOP and possibly Cython skills. 

While I find the “Molecular volume and surface analysis” particularly interesting, I would like to propose and develop the following idea: “Implementation of an electrostatics module in MDA”. Specifically, I would like to exploit the point charges attribute of the topologies to evaluate various electrostatic properties, e.g. electrostatic potential (ESP) on a grid (taking advantage of the griddata module already present in MDA), electrostatic interactions between groups, dipole evaluation, etc. 

I think this idea connects nicely to the “Molecular volume and surface analysis” project, since one could evaluate ESP on surfaces, thus possibly exploiting the same freeSASA library. 

If you think my idea could be of interest for the MDAnalysis team I am certainly available to either discuss further my proposal or work on your aforementioned project. 

Best regards,

Leonardo Barneschi

[LEONARDO BARNESCHI]

I forgot to share my GitHub handle: 
https://github.com/LeonardoBarneschi

[ialibay]

Hi Leonardo,

Welcome to MDAnalysis and GSoC. To get you started, we recommend that you get familiar with MDAnalysis' approach to the GSoC application process (see the blog post https://www.mdanalysis.org/2021/03/09/gsoc2021/ and the FAQ https://github.com/MDAnalysis/mdanalysis/wiki/GSoC-FAQ) and then work on an issue.

If possible, could you also provide us with your GitHub handle? This way we can consolidate any issues/PRs you contribute to with this introduction and any other interactions we have with you on the developers list.

We're happy to discuss your project idea in more details. Personally I think it seems quite interesting, it would definitely form a nice addition to surface analysis. I would encourage you to start working on a draft of your proposal early so we can better understand the types of things you plan to implement.

Best regards,

Irfan

[ialibay]

> If possible, could you also provide us with your GitHub handle?

Apologies, I hadn't seen your second email come through before pressing send on my last email.

[ialibay]

Hi Leonardo,

This is just a reminder that the deadline for applications is April 13th. We have you down as having fulfilled the "merge a pull request" requirement. Do feel free to share your draft application and we'll try to give feedback before the deadline.

Best regards,

Irfan