Tool: Minimize Structure

Minimize Structure energy-minimizes an atomic model or part of an atomic model, leaving the remaining atoms frozen in place. It is also implemented as the minimize command. The atoms are assigned types and associated force field parameters as described for Add Charges, and then the minimization is carried out using the OpenMM LocalEnergyMinimizer with the LangevinIntegrator. See also: Build Structure, tug, mouse modes tug and minimize

Minimize Structure automatically runs dockprep to perform several tasks to prepare the structure, including:

• deleting water molecules
• repairing truncated sidechains
• adding hydrogens
• assigning partial charges

To skip running dockprep or to use specific options of that command, use minimize instead of the graphical interface.

Minimize Structure can be opened from the Structure Editing section of the Tools menu and manipulated like other panels (more...).

Only a single atomic model can be specified; to combine multiple atomic models into one beforehand, see combine. Also restrict to selection indicates whether to limit minimization to the currently selected atoms within that model, leaving all others frozen in place.

• Minimize until convergence (initial default on) – whether to minimize to convergence regardless of how many steps it takes. If this option is turned off, a Maximum # steps can be specified, meaning to halt minimization after the specified number of steps has occurred or convergence is reached, whichever is sooner. Convergence is defined as when the root-mean-square of all force components falls to 10 or lower.
• Update structure during minimization (initial default on) – whether to update the structure periodically during the minimization; otherwise, 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.
• Report energies to Log (initial default off) – whether to report the energy in the Log, not just transiently in the status line

OK initiates the process and dismisses the dialog, whereas Cancel simply dismisses the dialog. Help opens this page in the Help Viewer. The settings last used are remembered across sessions as user preferences.