Master's lecture in Chemistry - Reynir Kristjánsson

The lecture will be streamed: https://us02web.zoom.us/j/83530072194?pwd=K1Y0QmFpY3BKbURwUXl1L2VTSndVQT09

Master's student: Reynir Kristjánsson

Title: The Effect of Dimensionality on Boosted Molecular Dynamics

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Faculty: Faculty of Physical Sciences

Advisor:  Hannes Jónsson, Professor at the Faculty of Physical Sciences

Also in the masters committee: Vilhjálmur Ásgeirsson

Examiner: Gísli Hólmar Jóhannesson

Abstract

Molecular dynamics (MD) calculations that are used to simulate rare events can take a long time and use up considerable amount of computational resources. One method to extend the timescale of these calculations is the hyper-MD method where boost energy, is used to give the system extra amount of energy without changing the saddle points on the energy surface and without creating new saddle points. The amount of timescale extension is measured by the so-called boost factor which is boosted time divided by the MD time. Higher boost energy gives higher boost factor. However, the boost factor decreases with the number of degrees of freedom of the system. In this study, both MD and harmonic approximation to transition state theory are used to see how the boost factor scales with the number of dimensions. The results show that there is a considerable decrease in the boost factor as the number of degrees of freedom increases and that this can be understood from a drop in the pre-exponential factor in the Arrhenius rate expression. This pre-exponential factor is connected to the difference between the entropy of the reactant state and the transition state and decreases because the entropy of the reactants state increases compared with the entropy of the transition state.