On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size.

ABSTRACT: Computational simulations, akin to wetlab experimentation, are subject to statistical fluctuations. Assessing the magnitude of these fluctuations, that is, assigning uncertainties to the computed results, is of critical importance to drawing statistically reliable conclusions. Here, we use a simulation box size as an independent variable, to demonstrate how crucial it is to gather sufficient amounts of data before drawing any conclusions about the potential thermodynamic and kinetic effects. In various systems, ranging from solvation free energies to protein conformational transition rates, we showcase how the proposed simulation box size effect disappears with increased sampling. This indicates that, if at all, the simulation box size only minimally affects both the thermodynamics and kin

SUBMITTER: Gapsys V 

PROVIDER: S-EPMC7481008 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature