GROMACS version:2020.1 and 2023.3
Hi,
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?
Thanks in advance,
Gianluca Dell’Orletta