TY - JOUR
T1 - Energetic and entropic considerations for coarse-graining
AU - Kidder, Katherine M.
AU - Szukalo, Ryan J.
AU - Noid, W. G.
N1 - Funding Information:
The authors gratefully acknowledge the essential contributions of Tommy Foley, M. Scott Shell, and Kate Lebold to the prior studies that are explicitly discussed herein. The authors also acknowledge former group members Michael DeLyser, Nick Dunn, Joe Rudzinski, and Wayne Mullinax, who made important contributions to the computational methods employed in these studies. The authors gratefully acknowledge financial support from the National Science Foundation (Grant nos. MCB-1053970, CHE-1565631, CHE-1856337) that made this work possible, as well as a fellowship to Kate Lebold from the Molecular Sciences Software Institute under NSF Grant No. ACI-1547580. Portions of this research were conducted with Advanced CyberInfrastructure computational resources provided by The Institute for Computational and Data Sciences at The Pennsylvania State University ( http://icds.psu.edu ). In addition, parts of this research were conducted with XSEDE resources awarded by Grant TG - CHE170062. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant ACI-1548562). Figs. 1-3, 11, and 15, and 16 employed VMD []. VMD is developed with NIH support by the Theoretical and Computational Biophysics group at the Beckman Institute, University of Illinois at Urbana-Champaign.
Funding Information:
The authors gratefully acknowledge the essential contributions of Tommy Foley, M. Scott Shell, and Kate Lebold to the prior studies that are explicitly discussed herein. The authors also acknowledge former group members Michael DeLyser, Nick Dunn, Joe Rudzinski, and Wayne Mullinax, who made important contributions to the computational methods employed in these studies. The authors gratefully acknowledge financial support from the National Science Foundation (Grant nos. MCB-1053970, CHE-1565631, CHE-1856337) that made this work possible, as well as a fellowship to Kate Lebold from the Molecular Sciences Software Institute under NSF Grant No. ACI-1547580. Portions of this research were conducted with Advanced CyberInfrastructure computational resources provided by The Institute for Computational and Data Sciences at The Pennsylvania State University (http://icds.psu.edu). In addition, parts of this research were conducted with XSEDE resources awarded by Grant TG - CHE170062. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant ACI-1548562). Figs. 1-3, 11, and 15, and 16 employed VMD [169]. VMD is developed with NIH support by the Theoretical and Computational Biophysics group at the Beckman Institute, University of Illinois at Urbana-Champaign.
Publisher Copyright:
© 2021, The Author(s), under exclusive licence to EDP Sciences, SIF and Springer-Verlag GmbH Germany, part of Springer Nature.
PY - 2021/7
Y1 - 2021/7
N2 - Molecular dynamics simulations often adopt coarse-grained (CG) models to investigate length- and time-scales that cannot be effectively addressed with atomically detailed models. However, the effective potentials that govern CG models are configuration-dependent free energies with significant entropic contributions that have important consequences for the transferability and thermodynamic properties of CG models. This review summarizes recent work investigating the fundamental origin and practical ramifications of these entropic contributions, as well as their sensitivity to the CG mapping. We first analyze the energetic and entropic components of the many-body potential of mean force. By adopting a simple model for protein fluctuations, we examine how these components vary with the CG representation. We then introduce a “dual potential” approach for addressing these entropic considerations in more complex systems, such as ortho-terphenyl (OTP). We demonstrate that this dual approach not only accurately describes the structure and energetic properties of the underlying atomic model, but also accurately predicts the temperature-dependence of the CG potentials. Furthermore, by considering two different CG representations of OTP, we elucidate how these contributions vary with resolution. In sum, we hope this work will prove useful for improving the transferability and thermodynamic properties of CG models for soft materials.
AB - Molecular dynamics simulations often adopt coarse-grained (CG) models to investigate length- and time-scales that cannot be effectively addressed with atomically detailed models. However, the effective potentials that govern CG models are configuration-dependent free energies with significant entropic contributions that have important consequences for the transferability and thermodynamic properties of CG models. This review summarizes recent work investigating the fundamental origin and practical ramifications of these entropic contributions, as well as their sensitivity to the CG mapping. We first analyze the energetic and entropic components of the many-body potential of mean force. By adopting a simple model for protein fluctuations, we examine how these components vary with the CG representation. We then introduce a “dual potential” approach for addressing these entropic considerations in more complex systems, such as ortho-terphenyl (OTP). We demonstrate that this dual approach not only accurately describes the structure and energetic properties of the underlying atomic model, but also accurately predicts the temperature-dependence of the CG potentials. Furthermore, by considering two different CG representations of OTP, we elucidate how these contributions vary with resolution. In sum, we hope this work will prove useful for improving the transferability and thermodynamic properties of CG models for soft materials.
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U2 - 10.1140/epjb/s10051-021-00153-4
DO - 10.1140/epjb/s10051-021-00153-4
M3 - Review article
AN - SCOPUS:85111353646
SN - 1434-6028
VL - 94
JO - European Physical Journal B
JF - European Physical Journal B
IS - 7
M1 - 153
ER -