Hi all,
I’m trying to run a molecular dynamics simulation of deoxygenated hemoglobin in GROMACS, but I’m facing issues getting the simulation to run successfully beyond energy minimization and equilibration.
I’m using the gromos force field, which includes parameters for the heme group. While the topology generation and initial steps (minimization and NVT/NPT equilibration) complete without major issues, the production MD does not proceed as expected, and the system seems to stall or crash.
Could anyone please guide me on how to correctly set up a simulation of hemoglobin (deoxy form)? I’d especially appreciate suggestions on:
- Choosing an appropriate force field compatible with heme and protein,
- Handling the coordination state of the iron (Fe) in the deoxy form,
- Any examples or validated workflows for similar system