Distance-type reaction coordinates for modelling activated processes
A suitably defined distance is the simplest parameter for measuring the difference between two positions, orientations, and/or conformations of a molecular system. Distances also provide a first guess for the reaction coordinates of activated processes. It is shown here that mass-weighted distances possess remarkable mechanical and statistical mechanical properties. They allow us to restrict motions to internal coordinates of a molecule in a simple way where this demand makes sense. Moreover, the computation of free energy changes and rates is facilitated by simple explicit formulae. The numerical treatment of a rate process in a peptide, the ring flip of a phenylalanine, demonstrates the practical application of our results. It also indicates the role of internal friction in macromolecules and the need to consider transmission coefficients.
reaction coordinate free energy constrained dynamics targeted molecular dynamics thermodynamic integration