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MDAnalysis is a Python library to analyze molecular dynamics simulations.
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Bending modulus #4151

Open m-a-r-i-u-s opened 1 year ago

m-a-r-i-u-s commented 1 year ago

Dear Developers and Users of MDAnalysis,

We are aware that there is currently no official feature in MDAnalysis for calculating the bending modulus of lipid membranes. However, we have been working with several methods (e.g. https://pubs.acs.org/doi/10.1021/ja507910r) in our group to investigate membrane elasticity using coarse-grained and atomistic simulations. The application of these have been described in the following publications:

Considering the importance of this fundamental property and its applicability to a wider range of systems, we are interested in transferring some of our Python/Cython-based code to MDAnalysis to make it accessible to the community.

We would appreciate your feedback on the general interest and feasibility of incorporating these features into MDAnalysis.

Best regards, Marius Trollmann

aspitaleri commented 1 year ago

Hi - that would be very useful indeed!

IAlibay commented 1 year ago

Adding new analyses to the core library (especially when dealing with Cython) is a large undertaking. We've recently been pushing for an "ecosystem of downstream packages" instead through the idea of mdakits: https://github.com/MDAnalysis/MDAKits

Would this be something of interest instead?

m-a-r-i-u-s commented 1 year ago

Hi @IAlibay , I will take a look into the whitepaper. But it sounds also interesting for us at the first sight! The Cython part of the code is not that large and could be also integrated in plain Python.

m-a-r-i-u-s commented 1 year ago

Hello again @IAlibay , I readed the whitepaper and it sounded really interesting. I will give it a try to built such a MDAKit for the bending moduli calculation. However, it is my first time doing something like that, so it can take a little bit longer. ;)

Cheers.

hmacdope commented 1 year ago

@m-a-r-i-u-s Let us (the MDAnalysis team) know at any point if you are struggling or would like some clarification. We have a very active Discord including with a channel dedicated to MDAKits where you can go for help. :)

orbeckst commented 1 year ago

We also have an initial tutorial for making an MDAKit at https://mdakits.mdanalysis.org/makingakit.html

As @hmacdope said: please ask, we’re happy to help!