“I have performed molecular dynamics simulations for some proteins using GROMACS 2021. Now I plan to run simulations for other proteins using GROMACS 2024 and compare the dynamics of these systems. Will using different GROMACS versions for the simulations introduce inconsistencies or errors in the comparison? Should I rerun the older simulations with GROMACS 2024 to ensure consistency, or are there alternative approaches to address this?” i use CHARMM GUI to generate files (same mdb files (minmization-equlibration-production)
All GROMACS versions sample the same energy landscape given by the force field and toplogy and use the same algorithms (unless you changed mdp settings), so the results are comparable.