Accelerating rare events using temperature programmed molecular dynamics: a review

ABSTRACT

Uncovering the atomic scale mechanisms and their rate constants is often the first step towards understanding the dynamical behaviour of a material. Over the years, the molecular dynamics (MD) method has been a reliable workhorse by providing such kinetic information. However, when atomic scale events happen rarely at timescales accessible to MD it is more useful to apply a MD-based rare-event acceleration technique. We review a rare-event acceleration technique called the Temperature Programmed MD (TPMD). TPMD has been particularly effective with thermally-activated rare events on corrugated energy landscapes. Several fundamental aspects of the TPMD method are discussed including the temperature programme, deconvoluting the TPMD output to recover the rate constants for kinetic pathways, reconstructing unbiased dynamical trajectories from TPMD, as well as new schemes to optimise TPMD calculations. Sample scripts demonstrating the implementation of TPMD using the LAMMPS package, source codes for analysis, and user instructions have been provided.

KEYWORDS:

• Rare events
• molecular dynamics
• activated process
• kinetics

Acknowledgement

SS created LAMMPS scripts for performing TPMD, and scripts for detecting transitions. AC wrote codes for analysis of first passage times. SS and MJ performed TPMD calculations. SS and AC wrote the review article. All authors read the manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

ORCID

Abhijit Chatterjee http://orcid.org/0000-0002-3747-8433

Additional information

Funding

The author acknowledges support from the Science and Engineering Research Board, Department of Science and Technology, India [grant number EMR/2017/001520].