This protocol implements geometry optimization. There is a lot of options provided but the default setup was tuned to provide good results in almost any system.
The default setup is applicable to wide range of systems - the only adjustment needed might be setting the convergence thersholds using the opt_quality keyword. The default value of 1.0 is reasonable for common optimization of rigid molecules, for flexible systems or non-covalent interactions, tighter convergence criteria are needed for obtaining accurate geometroies. It is recommended to set the opt_quality to 0.1.
The protocol implements optimization in Cartesian (default), redundant internal and z-matrix coordinates. Only the optimization in Cartesian coordinates should be considered stable and robust, the internal coordinates are under development and often fail in some cases.
Cuby can now build z-matrix automatically from cartesian coordinates but it is not guaranteed that the generated z-matrix will work well for optimization. The use of z-matrices is thus recommended only for cases where user-supplied z-matrix is used. The advantage of z-matrices is that it is easily possible to optimize only specified internal coordinates.
Cuby implements the P-LBFGS algorithm[1] that can accelerate the convergence of the optimization by calculating multiple points in parallel in each step. For details, refer to teh example below an to the original paper.[1] To use the optimizer, it is necessary to complile the linear algebra extension with a support of the UMFPACK library, the details are described on the page on installation.