Campus Units

Chemical and Biological Engineering

Document Type

Article

Publication Version

Submitted Manuscript

Publication Date

8-25-2015

Journal or Book Title

Journal of Chemical Theory and Computation

Volume

11

Issue

10

First Page

4586

Last Page

4592

DOI

10.1021/acs.jctc.5b00574

Abstract

The computationally expensive nature of molecular dynamics simulation limits the access to length (nanometer) and time scales (nanosecond) that are orders of magnitude smaller than the experiment it models. This limitation warrants a careful estimation of statistical uncertainty associated with the properties calculated from these simulations. The assumption that a simulation is long enough so that the ergodic hypothesis applies is often invoked in the literature for the computation of properties of interest from a single molecular dynamics simulation. Here, we demonstrate that making this assumption without validation results in poor estimates of the self-diffusion coefficient from a single molecular dynamics simulation of Lennard-Jones fluid. This problem is shown to be even more severe when the diffusion coefficient of macromolecules is calculated from a single molecular dynamics simulation. We have shown that conducting multiple independent simulations is necessary to obtain reliable estimates of diffusion coefficients and their associated statistical uncertainties. We show that even a “routine” calculation of the self-diffusion coefficient for a Lennard-Jones fluid, as determined from a linear fit of the mean squared displacement of particles as a function of time, violates the key assumptions of linear regression. A rigorous approach for addressing these issues is presented.

Comments

This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in Journal of Chemical Theory and Computation, copyright © American Chemical Society after peer review. To access the final edited and published work see DOI: 10.1021/acs.jctc.5b00574 . Posted with permission.

Copyright Owner

American Chemical Society

Language

en

File Format

application/pdf

Published Version

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