Scaling in Solvation: Implicit Solvent vs. Explicit Solvent
Professor Ray Luo
Department of Molecular Biology and Biochemistry
University of California, Irvine
Abstract
Implicit solvents have become increasingly popular in biomolecular
simulations. However their wide applications have revealed many limitations,
such as improper balance of secondary structures, over population of
salt-bridge interactions, and stability of proteins in molecular dynamics.
These well-known limitations of implicit solvents show that more
developments are still needed to fully establish the applications of
implicit solvents in biomolecular simulations. We have initiated efforts to
quantitatively and rigorously address how well implicit solvents can
approximate explicit solvents. We have studied whether implicit solvents
break down when scaling from small organic molecules to typical-sized
biomacromolecules. We have analyzed implicit solvents in the context of
molecular dynamics simulations on simple systems such as dipeptides and
peptides where conformational sampling is less challenging. We have found
overall a good agreement between implicit and explicit solvents when
consistent calibration and testing is performed. We have also noticed
limitations in implicit solvents that require further development.