Simulations of the beginnings of HCN polymerization

The research study investigated the free energy landscape of HCN oligomerization through competing pathways. The research data consists of results from quantum chemical calculations and input files for molecular dynamics simulations sufficient to reproduce the study. cp2k version 6.1 was used for simulations. Gaussian16 was used for molecular optimizations. PLUMED version 2.5 was used for analysis. gaussian_optimizations Folder contains gaussian16 outputs from optimizations of conformers, reactant and product complexes as well as transition states. reference_state_simulations Folder contains cp2k inputs for equilibration and production runs of all reference states (2,3,16,17 and 15) solvated in a box of liquid HCN and a CN-. plumed inputs are also included. ts-simulations Folder contains cp2k simulations: TSequilibration, committor analysis and umbrella sampling simulations, for reactions 1-5.