Protocol native_opt

This protocols allows performing a complete geometry optimization in the external software. Cuby's optimizer is not used and and only the final optimized geometry is retrieved.

Limitations

• No common way of controlling the optimization setup and accuracy
• External program may translate/rotate the molecule arbitrarily
• Cuby's options to freeze atoms etc. not applicable
• Modifiers can not be used

Advantages

If the limitations listed above are not an issue, using the native optimization may be more efficient, especially in calulations that are themselves very fast and the limiting step is the transfer of data between Cuby and the external program.

Optimization setup

Because each program implements the optimization differently, Cuby will run the optimization using its default setup (what applies also to the convergence limits) unless noted otherwise. To modify the setup, use Cuby's means of modifying the input for the external calculation directly (for interface x, there usually are keywords such as x_keywords, x_extra_input or similar).

Supported interfaces

So far, only selected interfaces implementing fast methods are supported:

• Mopac interface
• Amber interface

Keywords used

This protocol does not use any specific keywords

Other keywords used by this protocol:

• geometry_write_cuby_header
• pdb_extra_columns
• restart_file
• restart_file_append
• restart_file_converged