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.

Default setup

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.

Coordinate systems

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.

Parallel optimizer P-LBFGS

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.

Transition states

A simple optimization to transition state is available. It is based on following the normal mode corresponding to the lowest (most negative) eigenvalue of the Hessian. Such an optimization should start from a good guess of the TS structure. The TRIM optimizer with Hessian calculation in each step must be used. For now, optimization to TS works only in cartesian coordinates. See Example 4.

References

  1. Klemsa, J.; Řezáč, J. Chemical Physics Letters 2013, 584, 10–13.