kimmdy-dimerization-examples

Examples demonstrating the usage of the kimmdy-dimerization plugin including analysis scripts for quantum yield determination.

• data contains the extracted data such as rates, distances, angles (from KIMMDY or gmx angle/distance) or grid search results for parameter fitting
• graphics contains Images obtained from the raw data used in the manuscript (or the SI)
• input_structures contains the pdb input files for all structures as well as the equilibrated structures that were used as Input for the KIMMDY runs
• parametrization contains everything regarding charge and residue parametrization of the additional dimer residue - including the modified forcefield (which is based on OL21).
• scripts_and_setup contains all scripts / input files (besides structures) used to setup GROMACS or KIMMDY simulations and analyize them

Sample names different from the manuscript: ds_left and ds_right stand for left only or right only. ds_both in equilibration is the precursor for left 1st, left 2nd, right 1st and right 2nd. ds_both_pre in KIMMDY runs contains left 1st and right 1st (measure simulaniously, see SI) and ds_both_post in KIMMDY runs contains left 2nd and right 2nd (each simulation 'decided' for one of them, see SI).