The kick script is based on the stochastic search procedure originally defined by M. Saunders: "Stochastic Search for Isomers on a Quantum Mechanical Surface" M. Saunders, J. Comput. Chem. 2004, 25, 621 - 626.
This version needs additional input that defines molecular fragements.
Atoms belonging to a molecular fragment have the same number tag after xyz coordinates.
Benefits of this approach is getting a set of input structures that have basic connectivity
intact, while sacrficing un-biased exploration of the potential energy surface.
For each non-frozen fragment, a randomly directed vector is generated, where length of said vector
equals half of minimal distance value added to randomly chosen fraction of distance parameter.
After atoms of each fragment are displaced alongside fragment vector to a new position,
each non-frozen fragment is randomly rotated. This version partialy remebers relative initial
positions of each fragment, thus fragments "wiggle" from initial positions.
Articles published with this procedure in our group include:
"Racemization of oxazepam and chiral 1,4-benzodiazepines. DFT study of the reaction mechanism in aqueous solution"
L. Hok, L. Božičević, H. Sremec, D. Šakić, V. Vrček, Org. Biomol. Chem. 2019, 17, 1471-1479.
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