GSoC 2021 Introduction

[Aniruddha Seal]

Hi MDAnalysis Developers,

I am Aniruddha Seal, a third-year undergraduate in Chemistry(with Physics minor) at the National Institute of Science Education and Research(NISER Bhubaneswar), India. presently studying driving forces for phase separation in lipid membranes using Molecular Dynamics simulations.

I got to know of MDAnalysis during my freshman year internship, where I used it for water dynamics analysis (Translational and Rotational Dynamics). Here are some of the codes I wrote then, using MDAnalaysis for the same: https://github.com/aniruddha-seal/Water-Dynamics-Analysis For my present work also, I am using MDAnalysis as a tool for doing some parts of setting up a simulation system containing a multi-component lipid bilayer membrane with artificial lipid topology. We have made a tutorial for using it, which can be found at : https://github.com/aniruddha-seal/AA-Artificial-Lipid-Bilayer-Tutorial

Of the projects en-listed on the GSoC 2021 page: I am particularly interested in working on Project 2: Generalize Groups, implementing a Ring Class, and related Analysis. But I haven't read about Graph Theory formally. The project on Molecular volume and surface analysis also seemed quite interesting. I would like to start with incorporating the FreeSASA library in MDAnalysis, in the process in case we better efficient algorithm to calculate the surface volumes to can switch to that. One more project idea I had in mind was including an NMR Chemical Shift Prediction Tool in MDAnalysis.( in particular had an interest in implementing GNN from Andrew White's Group:  https://www.biorxiv.org/content/10.1101/2020.08.26.267971v1.abstract) An immediate application, which I can think of would be to do Chemical Shift guided simulations. At present, I don't think we have a platform where we can do both, that is estimate the Chemical Shift as well as incorporate that information in simulations input files. Pardon me for this sloppy explanation!!

I look forward to working with you all and contribute to this wonderful library. 

Regards,
Aniruddha 

GitHub: https://github.com/aniruddha-seal

[Oliver Beckstein]

Hi Aniruddha,

Welcome to MDAnalysis and GSoC. Great to hear that you’ve been using MDA for your work and thank you for sharing the link for your tutorial.

Just in case if you havent done so already, please have a look at the blog post and the FAQ ) and then work on an issue. We’re also happy to talk about projects when you have specific questions. The chemical shift analysis sounds interesting. Using it for guided simulations is probably going to be more challenging because you have to interoperate with an MD engine. However, there’s a PR in progress to interoperate with OpenMM (#2917) which might help eventually.

Best,

Oliver

--

Oliver Beckstein (he/his/him)

email: orbe...@mdanalysis.org
twitter: @orbeckst

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