I am experiencing a reproducibility issue between two versions of GROMACS and would appreciate your input.
We performed molecular dynamics simulations of tripeptides using GROMACS 2020.1 with the CHARMM36m force field. Over time, we observed the formation of small peptide clusters, as expected.
However, when restarting the simulation from the last frame of the trajectory and running it with GROMACS 2023.3 (using exactly the same parameter files, topology, and input settings), the clusters disaggregate very quickly.
Do you have any suggestions of what could be the cause of this issue?
Thank you for your answer.
No, I haven’t yet continued the simulation with GROMACS 2020.1, but I did try using version 2021.2, and the results look consistent — the clusters remain stable throughout the simulation (up to 750 ns).
On the other hand, with version 2023.3, we observe an unexpected behavior where the clusters rapidly disaggregate.
I understand the need for running replicates. However, the results so far are quite unusual — the disaggregation effect occurs within just ~100 ps, which seems physically unreasonable.
For clarity, I’m attaching the SASA profiles from the simulations run with GROMACS 2020.1 and 2023.3.