Over the years, stochastic search procedure for starting structures on the potential energy surface has evolved from 50 lines of Fortran code with simple and rugged idea, to a variety of different flavors and variants.
Here, some of those are presented, and implemented in a web-page variant.
To choose the right variant, a common example with three water molecules with in-line orientation to each other is chosen. Click Visualize to preview starting coordinates. Several options are given, according to
different algorithms here presented. Please choose among the provided options. After clicking Generate button, newly generated output (description and visualization) will showcase the strengths and flaws of each approach.
More info about code can be found in the More Info section, as well as found code examples from other research groups using local variants of the original procedure.
Slight change has been done on the scripts here used; minimal distance parameter between any two atoms previously was defined by user. Now it is automatically set at 90% of sum of covalent radius's of each pair. Bonds
are portrayed for inter-atomic distances between 90% and 110% of sum of covalent radius's of each pair.
Help from Valerije Vrček (discussion), Hendrik Zipse (documentation, suggestions) and Vasily Korotenko (testing) is greatly appreciated. Please report all suggestion, changes, improvements, and usage to dsakic@pharma.hr