Inferring free-energy barriers and kinetic rates from molecular dynamics via underdamped Langevin models

Abstract

Rare events include many of the most interesting transformation processes in condensed matter, from phase transitions to biomolecular conformational changes to chemical reactions. Access to the corresponding mechanisms, free-energy landscapes and kinetic rates can in principle be obtained by different techniques after projecting the high-dimensional atomic dynamics on one (or a few) collective variable. Even though it is well-known that the projected dynamics approximately follows – in a statistical sense – the generalized, underdamped or overdamped Langevin equations (depending on the time resolution), to date it is nontrivial to parameterize such equations starting from a limited, practically accessible amount of non-ergodic trajectories. In this work we focus on Markovian, underdamped Langevin equations, that arise naturally when considering, e.g., numerous water-solution processes at sub-picosecond resolution. After contrasting the advantages and pitfalls of different numerical approaches, we present an efficient parametrization strategy based on a limited set of molecular dynamics data, including equilibrium trajectories confined to minima and few hundreds transition path sampling-like trajectories. Employing velocity autocorrelation or memory kernel information for learning the friction and likelihood maximization for learning the free-energy landscape, we demonstrate the possibility to reconstruct accurate barriers and rates both for a benchmark system and for the interaction of carbon nanoparticles in water.