Tabulated non-bonded potentials

User discussions
1

GROMACS version: 2022
GROMACS modification: No

Hi,

Is there any (short/mid-term) plans to re-implement tables in GROMACS?

We are thinking of doing some development with the Martini FF using tabulated NB potentials with earlier GROMACS versions. However, that only makes sense if tables will be back to GROMACS in foreseeable future versions.

Thanks!

2

Hi,
As far as I understood, there is not short term plan to re-implement tabulated potential. @pbauer may know more on mid/long term plan.
Anyway to use tabulated non-bonded potentials, you can use version 2018 (but maybe you know already)
Best regards
Alessandra

3

For what it’s worth, LAMMPS has tabulated non-bonded potentials. It might be slower than an equivalent GROMACS computation (especially on CPUs), but at least the feature is portable across hardware platforms (i.e. GPUs).

MARTINI was designed to be 1:1 compatible with biomolecular atomistic force fields, with portability in mind. Other CG force fields have tried different approaches, e.g. sacrifice portability for accuracy by using different functions than those of atomistic force fields. You would probably find that many of those force fields have a LAMMPS implementation using e.g. dedicated potential functions or tabulated ones.

With some exceptions, it has been standard practice for people developing those force fields to also invest effort developing the code needed to run them.

I don’t know how much work is required by the GROMACS core team, but certainly it’s not trivial or it’d have been done already. If there is a broad demand to use GROMACS with force fields other than atomistic and MARTINI, they may consider adding it back in the future.

Giacomo

4

Thanks for the info Alessandra! Indeed, I am aware that we can use version 2018. But it would be good to know that our development would later be supported modern GROMACS versions in the future. @pbauer , any more insight on the topic?

@giacomo.fiorin , thanks. I am indeed aware that we can use other software for this purpose, but as you mentioned, compatibility is important for any Martini development, and for that reason, we like to stick to GROMACS (as long as it is possible).

5

Hello @selimsami,

sorry for the long silence here. The issue with the tabulated potentials is that we can’t just write a direct replacement for the verlet kernels, but need some major work on the internals for having a proper integration in GROMACS. This has been in the work for a while, but it still work in progress. I hope we can share a version with them integrated when the GROMACS 2023 beta comes out in autumn this year, but I’ll make sure to keep the community informed here anywhere.

I know that this has been a major issue with GROMACS since we removed this with the 2019 release, and that it is something we need to urgently address.

Cheers

Paul

6

Hi @pbauer,

Thanks for the update, this is very useful!
We’ll keep our eyes open for the 2023 beta then.

Cheers
Selim

7

hi everyone,
any update on reintegrating tabulated potential in gromacs 2024?

8

Our hope is to reimplement tabulated nonbonded potentials during 2024, i.e., for GROMACS 2025. But since we’ve been hoping to have time and resources to do that for many releases now, I will definitely not promise anything.