Residence Times from Molecular Dynamics Simulations

Abstract

In this work, efficient methods are proposed for the calculation, from molecular dynamics trajectories, of residence times (RTs) and related quantities. One of these was designed to obtain RT distributions, from which mean residence times (MRTs), residual time distributions, and mean residual times can be computed. This method does not require the assumptions and approximations made by the most commonly used methods. Its link to the most popular method in the literature is identified. It is shown how the much faster new method can be used as a replacement for the latter and the advantages of doing so. Also, a prescription for estimating the uncertainty in the MRTs obtained though the proposed method is provided. Another even faster method for the calculation of the MRTs, their uncertainties, and the mean residual times is also proposed. It yields exactly the same results as the first one but does not allow to obtain the mentioned distributions. Another very popular method, based on autocorrelation functions, for computing MRTs is analyzed in terms of its assumptions and approximations. An alternative, also based on autocorrelation functions, which is faster and requires fewer assumptions is presented. A prescription for the calculation of the uncertainty of the MRTs obtained with the latter method is also provided. In the literature, there are a few methods to discard short transient escapes. Here, an algorithm is suggested that is much faster than the most used one and allows a more integral treatment of the process. Also, it is more widely applicable because it is a preprocessing step that can be used in conjunction with any of the proposed methods mentioned above. The main disadvantage of these two approaches to discard brief escapes is that the maximum duration allowed for an escape to be considered transient appears as a parameter to be determined for the particular system under study. As an alternative, a parameter-free method of a similar character is also proposed to estimate the mean residence time of particles that reached a constant probability of leaving the region of interest.