Geometry optimizations

Geometry optimization algorithms aim to identify low-energy structures, a process of paramount importance in computational chemistry. EasyHybrid allows the use of various methods implemented in pDynamo, including the conjugate gradient algorithm, steepest descent, L-BFGS, quasi-Newton, and FIRE.

The Geometry optimizaton calculations can also be performed by accessing:

Main Menu > Simulate > Geometry Optimization

An overview of the window for Geometry optimizaton window can be seen in Figure 1.

In EasyHybrid, the reference system is determined by the active radiobutton in the treeview of the main window (note that each system is associated with a reference color).

• Coordinates: the set of coordinates used as the starting point. The combobox only displays objects associated with the selected system (if there is more than one frame, the last one is used).

• Method: the optimization algorithm: Conjugate Gradient, Steepest Descent, L-BFGS, Quasi-Newton or FIRE. Conjugate Gradient and L-BFGS are good general-purpose choices for large (MM or QC/MM) systems; Steepest Descent is robust for relaxing very distorted structures; Quasi-Newton is efficient for small systems; FIRE is a dynamics-based minimizer that is stable on rough energy surfaces.

• Log Frequency: how often (in iterations) the progress of the optimization is written to the log (default: 5).

• Maximum Iterations: the maximum number of optimization steps (default: 600). The optimization stops when this number is reached, even if it has not converged.

• RMS Grad. Tolerance: the convergence criterion: the optimization finishes when the root-mean-square of the gradient falls below this value, in kJ mol-1 Å-1 (default: 0.1). Smaller values give more tightly converged structures at the cost of more steps.

Saving the trajectory

If the Save Trajectory checkbox is active, the intermediate structures are written to disk:

• Working Folder: the folder where the trajectory will be saved.

• Trajectory Frequency: how often (in iterations) a frame is saved (default: 10).

• Format: the trajectory format (pDynamo / pkl, saved as a .ptGeo folder).

After clicking Run, the optimized coordinates are added to the system as a new object in the main window, so the initial and optimized structures can be compared. Atoms marked as fixed (see Fixing atoms) are kept frozen during the optimization.