GROMACS version: 2025.x
GROMACS modification: Yes/No
Good morning (afternoon, or evening), everyone.
We are attempting to revive an old project that relied heavily on the now-defunct “g_mmpbsa” tool within the GROMACS environment. Then we are interested in developing a project over the next six months to overcome these obstacles and restore a distribution featuring an active “g_mmpbsa” tool, similar to its previous implementation. As we know, current public GROMACS interfaces (especially following recent refactoring) do not directly support all the requirements needed for “g_mmpbsa”, such as reading binary files, data typing, accessing internal structures, assembling simulation files, and manipulating topological information. However, these routines are essential for running the MM/PBSA calculations that the program performs. Although these functions are not publicly exposed via the API, their definitions and implementations remain available in the “libgromacs” library (as verified with the `nm` command in Unix environments). Furthermore, the corresponding header files are still present in the GROMACS source code (under “gromacs/src/gromacs”) and are distributed across subdirectories, as in previous versions.
Initially, we would like an assessment of the short-term (1-2 years) and long-term (next 5 years) feasibility of this initiative. The general idea is to include the “internal header” files from the GROMACS (version 2025.x) source code when compiling “g_mmpbsa” in Linux Mint 22 (Ubuntu) environment, thereby allowing the program to access the subroutines declared in those headers. In this model, the final linking stage with “libgromacs” would be responsible for resolving the implementations of the functions previously declared in the headers. We would appreciate the opinion of someone with deep knowledge of the GROMACS general ecosystem and (if applicable) any insights into what might (or might not) work with this proposed approach.
Of course, it would also be extremely valuable to receive feedback on any existing initiatives or groups working on similar efforts.
Thanks to all in advance,
Jorge H.F.