Energy Minimisation

From wiki.gromacs.org

This is a non-dynamical calculation used to find a local potential energy minimum near the starting structure. It uses a force field and mdrun, even though molecular dynamics are not being performed. It is usually needed to do one of these calculations before attempting MD, because the process of solvating your initial solute structure usually introduces some bad contacts that need to be relaxed before you attempt to heat the system, ie. give it kinetic energy.

[edit] Conjugate gradient minimization and constraints

The combination of a conjugate gradient minimization algorithm and constraints is not implemented in GROMACS. Either use a different minimization algorithm or don't use constraints.