The minimize command energy-minimizes atomic structures.
The corresponding tool is
Minimize Structure.
Only a single atomic model should be specified; to combine multiple models
into one beforehand, see combine.
The atoms are assigned types and associated force field parameters
as described for addcharge, and
then the minimization is carried out using the OpenMM
LocalEnergyMinimizer with the
LangevinIntegrator.
See also:
Build Structure,
tug,
mouse modes
tug and
minimize
By default (dockprep true), the minimize command calls dockprep to perform several tasks to prepare the structure beforehand, including:
The dockprep command options can also be used in the minimize command to control these processes.
The maxSteps option sets the number of minimization steps (default 0, meaning that minimization will continue until convergence regardless of how many steps it takes). If a maximum number of steps (>0) is specified, minimization will still end at convergence, even if fewer than the specified number of steps have been taken. Convergence is defined as when the root-mean-square of all force components falls to 10 or lower.
The liveUpdates option (default true) indicates whether to update the structure periodically during the minimization; if false, the structure will not be updated until the minimization ends. The current update interval is every 100 steps, at the same time the energy is reported in the status line. Messages in the status line, however, are only transient. The logEnergy option (default false) indicates whether to also report the energy in the Log.