November 1st, Developer bi-weekly videoconference

Dear GROMACS developers,

Our next biweekly meeting will be on 2023-11-01T16:00:00Z. At the moment we have two open slots, so if there’s anything you wish to discuss please comment below (or let me or Berk know)!

Berk/Magnus: general issues and news from Stockholm
Alexey Nesterenko: molecular stress
Giacomo, Jérôme, Hubert: Colvars
Open slot

Note that we have a new Zoom room since June:

Join our Zoom Meeting (magic link)

Meeting ID: 692 7708 9234
Password: gmxdevs

Join by SIP:

See you next week!

Hello everyone! I am Alexey Nesterenko.

Yes, I would like to attend to speak about molecular stress. I give the short abstract here.

Stress computations are a very promising branch of molecular dynamics simulations. There is one very widely used tool, which helps us to extract information about stress from ready MD-trajectories.

However, stress computations require computing virial from bonded forces, nonbonded forces and constraint forces and redistributing it depending on the geometry and interaction type. That in turn requires some pointers to be passed deep inside computational kernels. The golden standard in this field is GROMACS-LS is forked from GROMACS 5.1 and as far as GROMACS is being developed, it’s now very hard to rebase GROMACS-LS to the modern version. The authors rebased it to the 2016 version but that was it.

In our lab (Miettinen group at the University of Bergen), we are developing a slightly different theory of stress computations (currently it’s branched from 2020.3), but we are facing exactly the same problems as GROMACS-LS developers.

I would like to talk about how stress computations can be included to keep them updated. I realize that maybe the core developers may not want stress computations to become a part of the distribution, that’s why I will offer to think about including at least some small interface into CPU computation kernels which allows stress code developers to develop their code in a separate folder without touching the core codebase. I suppose that it’s possible to find a solution, which will not affect performance and allow people like us or GROMACS-LS creators to develop stress computation utilities, which are easy to keep updated. That is what I want to discuss.

Just a reminder that our next biweekly GROMACS developer meeting will take place tomorrow at 5pm (Stockholm time)! We still have two open slots so please let us know if there’s anything you wish to discuss!

Looking forward to seeing you tomorrow!