GROMACS version: 2021, 2022, 2023,2024
GROMACS modification: No
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This is a conundrum for me, and I was wondering if other people have encountered it.
I run pretty milquetoast simulation on cluster. I prepare the system using the charmm-gui service and modify the mdp files according to my needs.
I have noticed that proteins solvated in water run perfectly well in all versions of GROMACS. However, systems that are embedded in lipid crash immediately during production in any Gromacs version other than 2021.
The equilibration steps work perfectly in all versions (using Berendesen thermostat and the protein is coupled to the lipid). When in production (using Parrinello-Rahman) the simulation crashes on the first step claiming atoms moved between cells and more equilibration is required (I slowly equilibrate for more than 1ns). When I run it using Gromacs 2021 with the same parameters, it runs without a hitch.
Again, water-solvated proteins work in all versions.
Has anyone encountered this phenomenon?