期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 38, 期 16, 页码 1353-1361出版社
WILEY
DOI: 10.1002/jcc.24754
关键词
molecular dynamics simulations; protein; polymer; solvation
资金
- National Science Foundation [CHE-1012651, ACI-1053575]
- MRSEC Program of the National Science Foundation [DMR 1121053]
- NSF [MCB-1158577]
- Extreme Science and Engineering Discovery Environment - XSEDE [TG-MCA05S027]
- Center for Scientific Computing from the CNSI, MRL: an NSF MRSEC [DMR-1121053, NSF CNS-0960316]
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. (c) 2017 Wiley Periodicals, Inc.
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