Guidelines for Free-Energy Calculations Involving Charge Changes.

ABSTRACT: The Coulomb interactions in molecular simulations are inherently approximated due to the finite size of the molecular box sizes amenable to current-day compute power. Several methods exist for treating long-range electrostatic interactions, yet these approaches are subject to various finite-size-related artifacts. Lattice-sum methods are frequently used to approximate long-range interactions; however, these approaches also suffer from artifacts which become particularly pronounced for free-energy calculations that involve charge changes. The artifacts, however, also affect the sampling when plain simulations are performed, leading to a biased ensemble. Here, we investigate two previously described model systems to determine if artifacts continue to play a role when overall neutral boxes ar

SUBMITTER: Petrov D 

PROVIDER: S-EPMC10809403 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature