title: Systematic derivation of implicit solvent models for the study of polymer collapse.
abstract: The conformational states adopted by a polymer chain in water are a result of a delicate balance between intra-molecular and water-mediated interactions. Using an explicit representation of the solvent is, however, computationally expensive and it is often necessary to turn to implicit representations. We present a systematic derivation of implicit models of water and study the effect of simplifying the representation of the solvent on the conformations of hydrophobic homopolymers of varying length. Starting from the explicit coarse-grained single site mW water model, we develop an implicit solvent model that reproduces the free energy of the contact pair between two hydrophobic monomers, an implicit solvent model that captures the free energy of contact pair minima, desolvation barrier, and solvent-separated minima, and finally, we consider vacuum simulations. We generate potentials of mean force for polymers of various lengths in explicit water, the implicit solvents and vacuum, using umbrella sampling and replica exchange molecular dynamics simulations. Surprisingly, vacuum simulations outperform the implicit solvent simulations, with the implicit model involving a desolvation barrier producing spurious extended polymer conformations. © 2017 Wiley Periodicals, Inc.
authors.affiliation: Department of Chemistry, The University of Utah, Salt Lake City, Utah, 84112-0850.
authors.forename: Bin
authors.initials: B
authors.lastname: Song
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, 93106.
authors.forename: Nathaniel
authors.initials: N
authors.lastname: Charest
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, 93106.|Department of Physics, University of California, Santa Barbara, California, 93106.
authors.forename: Herbert
authors.initials: H
authors.lastname: Alexander Morriss-Andrews
authors.affiliation: Department of Chemistry, The University of Utah, Salt Lake City, Utah, 84112-0850.
authors.forename: Valeria
authors.identifier: 0000-0002-8577-4675
authors.initials: V
authors.lastname: Molinero
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, 93106.|Department of Physics, University of California, Santa Barbara, California, 93106.
authors.forename: Joan-Emma
authors.identifier: 0000-0002-9801-9273
authors.initials: JE
authors.lastname: Shea
keywords: molecular dynamics simulations; polymer; protein; solvation