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Energy MinimizationTable of contentsThis 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. There are three methods of energy minimization currently implemented in GROMACS: Energy minimization in GROMACS is not useful for computing a single-point energy - see that link for recommended procedure. Conjugate gradient minimization and constraintsThe combination of a conjugate gradient minimization algorithm and constraints is not implemented in GROMACS version 3.3 or older. Either use a different minimization algorithm or don't use constraints. Starting with GROMACS version 4.0 constraints can be used with conjugate gradient minimization. |