Transition rates, survival probabilities, and quality of bias from time-dependent biased simulations

Karen Palacio-Rodriguez; Hadrien Vroylandt; Lukas S. Stelzl; Fabio Pietrucci; Gerhard Hummer; Pilar Cossio

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arXiv · 2109.11360

Transition rates, survival probabilities, and quality of bias from time-dependent biased simulations

Karen Palacio-Rodriguez·Hadrien Vroylandt·Lukas S. Stelzl·Fabio Pietrucci·Gerhard Hummer·Pilar Cossio

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Abstract

Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of the system is altered by the bias. With infrequent metadynamics it is possible to recover the transition rate of crossing a barrier, if the collective variables are ideal and there is no bias deposition near the transition state. Unfortunately, for simulations of complex molecules, these conditions are not always fulfilled. To overcome these limitations, and inspired by single-molecule force spectroscopy, we developed a method based on Kramers' theory for calculating the barrier-crossing rate when a time-dependent bias is added to the system. We assess the quality of the bias parameter by measuring how efficiently the bias accelerates the transitions compared to ideal behavior. We present approximate analytical expressions of the survival probability that accurately reproduce the barrier-crossing time statistics, and enable the extraction of the unbiased transition rate even for challenging cases, where previous methods fail.

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Karen Palacio-Rodriguez, Hadrien Vroylandt, Lukas S. Stelzl, Fabio Pietrucci, Gerhard Hummer, Pilar Cossio. 2021-09-23. Transition rates, survival probabilities, and quality of bias from time-dependent biased simulations. https://arxiv.org/abs/2109.11360

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