An algorithm for estimating kinetic parameters of atomistic rare events using finite-time temperature programmed molecular dynamics trajectories

A new variation of the temperature programmed molecular dynamics (TPMD) algorithm, called finite time TPMD (FT-TPMD), is presented. In this variation, a collection of independent molecular dynamics (MD) trajectories is generated, such that each trajectory is of a fixed duration of time and a transition from a given state of the system may/may not occur in a trajectory. This eliminates the requirement of a successful transition in each trajectory and on-the-fly detection of transitions needed in previous TPMD implementations. As a result, FT-TPMD can be easily implemented with standard MD packages, such as LAMMPS, for performing TPMD calculations. Compared to previous TPMD algorithm, FT-TPMD is shown to be computationally as efficient in some cases and better in others. In addition, several refinements are discussed that enable systematic detection of rare transition events, classification of states, and calculation of rate constants. A set of rules is devised to identify one or more atoms involved in a transition and disqualify recrossing events. (C) 2021 Elsevier B.V. All rights reserved.

Automated summary

FT-TPMD is a new variation of the TPMD algorithm that allows for easier implementation of TPMD calculations and shows improvements in computational efficiency. It also has the capability for systematic detection of rare transition events, state classification, and rate constant calculation.