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.

The Clathrate–Water Interface Is Oleophilic

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Waterlike anomalies in hard core–soft shell nanoparticles using an effective potential approach: Pinned vs adsorbed polymers

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Simulating Biomolecules: Festschrift to commemorate the 60th birthday of Charles L. Brooks III

“…[21] Finally, Shea develops a systematic approach to derive implicit solvent models for the study of polymer collapse. [22] Novel methodological developments have always been at the heart of Charlie's research program, and this is reflected in the research directions that his former students have taken. In this issue, Hirst assesses the calculation of protein IR spectra using an exciton model, [23] Woodcock probes the challenges of computing converged free energy differences [24] and Patel develops a novel charge equilibration formalism for treating charge transfer effects in MD simulations.…”

“…Olson presents membrane insertion mechanisms of fusion peptides from Ebola and Marburg viruses using the GBSW implicit membrane model and replica‐exchange molecular dynamics simulations . Finally, Shea develops a systematic approach to derive implicit solvent models for the study of polymer collapse …”