I have performed a long MD simulation of lipid rafts formation using MARTINI force field. After that I have converted the system to atomistic model (using built in CHARMM-GUI converter).
After all, I want to minimize the obtained system, but I got fatal errors from GROMACS, saying, that lipids in the membrane have some bad interactions. Then the programme stops working, because of very high energy of the system (even though it has not reached the set number of steps...).
I am wondering if I could change the constraints in .mdp file to "none" instead of "h-bonds"?
Justin Lemkul
You will still have to minimize with appropriate constraints later, otherwise the geometries may be incompatible with the subsequent dynamics that require the use of constraints.
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